There are 3 islands that you can extend your stay on in the Galapagos: Santa Cruz, Isabela and San Cristobal.
Most trips start/end at the Baltra Airport, which is right next to Santa Cruz Island. So, this island will have the most options for hotels, restaurants, renting kayaks and other gear, scuba diving and joining day tours to nearby islands (i.e. Floreana, North Seymour, Isabela, South Plazas, Santa Fe, and Bartolome). A good option if you are just going to spend a couple extra days in the Galapagos.
Isabela Island is the largest island in the Galapagos. They have a very small town named Puerto Villamil. Isabela is much more removed from the main tourism flow that Puerto Ayora and San Cristobal receive. It offers some great beaches, sleepy sandy streets and a more authentic feel of life in the Galapagos. There are definitely some good day trips to nearby sites, but less options for food and other activities. To extend your stay on this island requires a minimum of 3 days, but would be best with at least 4 days.
San Cristobal Island also has an airport; some cruises will start/end here. San Cristobal is known for great surfing. They also have day tours to nearby sites (i.e. Kicker Rock and other sites located on San Cristobal), but there are less options. Scuba diving is also available and scuba diving at Kicker Rock is great for both beginners and experts alike.
TRANSPORTATION BETWEEN THE ISLANDS:
– There are flights between Baltra (near Santa Cruz) and Isabela & between Baltra – San Cristobal (approx $180 per person, one-way), departing every day except Sundays.
– There are public ferries that transfer from Santa Cruz to Isabela departing daily at 2pm and from San Cristobal to Santa Cruz departing daily at multiple times. Rates are approximately $35.00 per person (one way)