Intra-island transportation is relatively straightforward. You can travel between Baltra or Santa Cruz and the other main islands of San Cristóbal and Isabela either by plane, ferry, or private boat (lancha). However, itineraries and prices often change.
The small airline, EMETEBE, flies a five-passenger plane between the main islands every day, if there are passengers. Tickets can be purchased at any of the airports or at the EMETEBE office near the port supermarket in Puerto Ayora (hours: 7:15-10:45, 14:00-18:00; telephone: 05-252-6177). The flight costs $65 one-way/$130 round-trip and lasts about 30 minutes.
Ingala operates a passenger ferry between Santa Cruz, San Cristobal and Isabela. 
Puerto Ayora - San Cristobal: Daily, 2 p.m.
San Cristobal - Puerto Ayora: Daily, 6:30 a.m.
Puerto Ayora - Isabela: Daily, 2 p.m.
Isabela - Puerto Ayora: Daily, 6 a.m.
All ferries leave from the municipal docks and cost $30 one-way.
If you are in a hurry or cannot acquire a space on the ferry, you can contract a private boat in any of the port towns. Private transportation will be more expensive. Prices are negotiable, but you should expect to pay between $80 and $100 one-way to either San Cristóbal or Isabela. However, it will be faster and most certainly guided, since local boat-owners love to share their knowledge with tourists. The capitanía, or port captain, should also be able to tell you which boats are going to these islands and their expected departure times, or just ask around.