There are lots of options for Galapagos cruises on small ships. When we went to Ecuador we were planning on doing one, however, it is so expensive - $500/pp for round trip flight from Guyaquil to get to the ship, then $100/pp national park fee, then the least expensive cruise fare we found was for 5 nights for around $750/pp and this was on top of what we already spent on our international flight and our stay in Quito - so we went to the Ecuadorian Amazon instead because it was less expensive (and this was in 2001 - I am sure it is much higher now).
Galapagos is on our bucket list so one day we will get there!
I am starting to plan. Looking for possibly a Cat. Would like to do something very small.