Most people think that the only way to go to Galapagos is on a cruise ship. We travelled to the Galapagos independently and had one month there for the price of a one-week cruise.
How to get to the Islands
If you go by cruise ship, they will also want to arrange your flight from mainland Ecuador and include the airfare in the price of your cruise. If you do not let them book your flight, an additional fee will be added to your cruise cost. The amount the cruise companies charge for a flight is about $500. We booked our flight directly with Latam Airlines for $250. Half the price that the cruise companies charge.
Whether going to the Galapagos, Chile, Europe, or Africa, I never use a travel agent or an online booking company. I book the flight myself directly with the airline. Not only is it a bit cheaper, but if something goes wrong, such as your return flight gets cancelled, the airline will not help you if you purchased your ticket from an agent or an online company. They will only help you if you purchased your ticket directly from them. (There are lots of great travel tips like this on mythatchedhut.)
At the airport on the mainland, you will have to go through two security checks. Once is the standard airport security you encounter at airports worldwide. But before doing this, you will have to go through a different kind of security to make sure you are not taking any plants or anything else that could harm the environment in the Galapagos Islands. This will cost you $20.
Upon arrival, you will be required to pay a $100 entry fee. This is for the maintenance of the National Park, which takes up 97% of the islands, which is pretty much the whole place except for the towns. This has to be paid in cash.
Accommodations
We booked accommodations at small hotels and on Airbnb. A fraction of the cost of luxury all-inclusive places, but I know that some people want luxury, but that is not why I travel. I can save enough money by using less expensive accommodations to go on another trip.
From the Airport to Puerto Ayora
The airport is on the tiny island of Baltra. You will want to get to the main city of Puerto Ayora. First, take a bus to the southern coast of Baltra. This will cost $5. You can purchase tickets right outside the airport.

After the short bus ride, you will need to take a very short ferry ride to the island of Santa Cruz. This will cost $1. Your luggage will be loaded on the roof of the ferry.
After crossing the channel, you will need to take a bus or taxi to your accommodation in Puerto Ayora. The bus is $5, and the taxi is about $20, but is well worth it. The taxis are actually pick-up trucks. This is not so good if it is raining, as your luggage will be in the back of the truck.
The good part is that they will take you directly to your accommodation, and you won’t need another taxi when you get to the city if you take the bus. It is also more comfortable, and you can leave right away instead of waiting for the bus. (The little channel between the two islands is called a “canal” by locals. This might be correct in Spanish, but in English, a canal is a human-made waterway, such as the Panama Canal or the Suez Canal. A channel is a natural waterway, such as the English Channel between England and France.
Make sure you have the correct change, especially for the ferry. Ecuador does not have their own currency and uses the U.S. dollar. The one-dollar coin is in common use in Ecuador, but not so much in the USA.
Getting Around

We went to El Chato to see the free-roaming Giant Tortoises, which is in the centre of the island. Tours to El Chato are available for a couple of hundred dollars, but you don’t need it. We simply took a taxi there for about $20.
We also took a taxi to various places to go hiking in the forest, and we hiked up a volcano on the island.
You don’t want to miss the Darwin Centre, which is within walking distance of the town.
Getting to other Islands
Isla Seymour Norte

Take a boat trip to the island of Seymour Norte, which is north of Baltra. Here, you will get a chance to see marine birds nesting. The birds are very tame, and you can get within a few metres of them. Birds that you will see include the Great Frigatebird chick (photo above) and Blue-footed Boobies nesting with chicks, and many others.
Isla Bartolome
Take a day trip to Isla Bartolome. This mostly barren island of volcanic rock and ash is fascinating. The boat ride to Bartolome is very nice and offers the opportunity to see many bird species at sea and on the islands

Inter-Island Ferry
Getting to other islands is cheap and easy. There is a ferry service that leaves twice a day from the port in Puerto Ayora to other main islands. You can buy a ticket from any of the many travel agents along the main street. This will cost about $35, and I recommend buying it at least one day in advance, as the ferry might be full.
The ferry is fast and cheap, but the ride is rough. The small boat will bounce around a lot. Be sure to take medicine if you are prone to motion sickness, or maybe even if you are not. (Tip- get in line early to get a seat near the front of the boat, which bounces around a lot less than the back.
Cruise vs Ferry
The cruise ships are not giant ships like cruise ships in other places. They are mostly just yachts that hold about eight passengers plus crew. Travel between islands is much more comfortable than on the ferry and includes meals, but you will have to stick to their itinerary.
You will spend a lot of time at sea. You will go ashore probably once or twice a day for a couple of hours. On most tours, several hours per day are devoted to snorkelling, which is okay if that is your main objective for the trip. With independent travel, you go where you want, when you want and at a fraction of the cost. The disadvantage is that you have to arrange everything yourself, and it will not be as comfortable as a yacht cruise. Another difference is that the cruise ships can go to remote islands that you cannot get to on your own, but you will be missing very little if you don’t go there.
Isla Isabella
Isabella is our favourite of the Galapagos Islands. The little town of Villamil is a pleasure to stroll around, and we had some excellent seafood meals at the many great restaurants. Sampling the local cuisine is another advantage of independent travel. If you go by cruise, you will have all your meals on the ship. I was really amused by the musical garbage truck that broadcast music while picking up the garbage.

We rented an Airbnb overlooking a pond. We had a nice view of Flamingos on the pond every morning right from our room. You won’t see that on a cruise.
Here is the place to search for on Airbnb: Private room in serviced apartment in Puerto Villamil, Ecuador, Hosted by Teresa Tupiza. It is just a short walk from there to the main street in town. Well, anywhere in Puerto Villamil is just a short walk away. We spent a wonderful week there.
If you are really fit, you can go on a guided hike up the Volcano, not far from town. But there are many easy hikes along the coast. You can take a short boat ride to an island to see the rare Galapagos Penguin.
Inter-island Flights
Another way to get around the islands is by air. To get from Isabela to Santa Cruz would involve two of the horrible ferry rides, with an overnight stop in Puerto Ayora. We decided to fly with a tiny four-passenger aircraft. It was expensive, but even so, the total expenses were much lower than a cruise.
Santa Cruz
From Puerto Banquerizo Moreno on Santa Cruz, you can take day trips around the island for sightseeing or birding. This is a colony of Red-Footed Boobies at the north end of the island. You can also take a ferry to Isla Espanola to see the rare Wandering Albatross.
Summary
The Cruise ships. Going on a cruise around the Galapagos Islands has some advantages. Everything will be arranged for you. Making all the arrangements yourself can be daunting for some people, but personally, I enjoy the planning stage, anticipating all the things we will do and see. This is a great option if snorkelling is of high priority for you. You will spend a week or more aboard a small yacht with several other passengers.
You might make some lifelong friends, or you could be stuck with someone you hate. Keep in mind that Galapagos cruise ships are actually just yachts. There is no fancy dining room, and the quarters are tiny. Imagine spending a week in an area the size of your living room with six other people. You will spend the vast majority of your time on the ship and will spend only a few hours each day on land. For me, this is definitely not enough to explore and experience the cuisine and culture, go hiking, and see wildlife.
Independent Travel: Travelling on your own has a few disadvantages. You have to arrange everything yourself, and moving from one place to another can be a hassle. However, I think the advantages outweigh the benifts of a cruise.. First of all, it is much cheaper, costing only a fraction of the cost of a cruise. But that can be increased if you stay in expensive hotels. But even then, it would be much cheaper than a cruise. You can go where you want, when you want, and stay as long os yoiu want. We spent a week each on the three main islands. We often packed a lunch and went for day-long hikes along the coast. You can’t do that if you are on a cruise.
Day trips by boat instead of a cruise
Some places are accessible only by boat. If you don’t take a cruise, you may not be able to see them. This is not true. From the major towns, you can take day trips to other parts of the island and many of the smaller islands. We took many one-day excursions to remote places accessible only by boat.
So, it comes down to personal choice. Some people love the cruises. Personally, I much prefer to travel independently, see things that people on ships will never see, and spend my time on land, not at sea. Although the cruise ships visit some remote islands I did not see, I did not think it was worth the expense and time to spend a few hours there.