We just got back from a 12 day land based cruise using Surtrek out of Quito - and we had a marvelous time. Thought I would share our experience...
First-If possible, I would try to go land vs boat. As many have discussed on other forums, its much better for the local economy versus cruises ($ goes to mainland or foreign owners). You also can do more on each island, have way more flexibility, and judging from the bumpiness of our boat transfers, I don't think I would have enjoyed 8 days on a boat. Plus, we wanted a more active vacation, so land-based lends better.
Surtrek: I researched quite a bit, and this was the best level of service and price that I found. Some took forever to get back to you (had to go through middlemen) and others just wanted you to buy an 8 day cruise. Veronica at Suretrek went above and beyond the call of duty. We really customized our trip so I was in contact with them daily for a couple of weeks. During the trip, she called regularly to make sure we were having a good time and gave instructions to our hotels. We were able to change some daily activities, but I would warn that it's generally difficult to do so if you prepay. Suretrek was the most cost effective I found (unless you found hotels, tours, airfare on your own), and offered the highest level of customization. Much cheaper than cruise, and I felt better for our needs. If you use them, ask for Veronica!!
Hotels: We stayed at Miconia (San Cristobal), La Casa De Marita (Isabella), and Angermeyer Waterfront Inn (Santa Cruz). All in all, pretty good. La Casa i think was a bit overrated (theres several good places on the island), and Waterfront was by far our favorite.
Tour Operators: We really liked Sharsky in San Cristobal (young crew, very accomodating). Hotel San Vincente we were not too happy with (caution their loose definition of the term "bilingual"), but they seemed to be the only game in town. Scuba Iguana was great in terms of the dive/snorkel tours and guides themselves, but so-so when it came to booking other 3rd party tours. Overall - we were pretty happy with them.
Hope this helps - we had a wonderful time. Let me know if you have any questions during your vacation planning...