Yes, it is possible; there is a local airline specialized on inter-island flights; they fly a small aircraft (Cessna plane) 3 times a week between Baltra Island and Isabela Island (Puerto Villamil) as well as between Baltra and San Cristobal Islands Last we heard, fares were a little over $135.00 one way per person so if you have the money and not the time, this is a great way to get from island to island.
You can also charter hourly planes between US$450 and US$ 600 (rates are subject to verification), but can gladly cater this service for you!