We went to Galapagos in January, 2011. It was our favorite trip. That's a good time to go for several reasons: US schools were in session so there were no families with children on the ship, the weather is dry so there were almost no insects bothering us and the seas were flat calm.
We researched the tour providers and went with Metropolitan Touring, which is an Ecuadorean company. The US tour companies basically resell local tours from companies like this one at a markup. From our research it seems that everyone likes the boat he was on a lot. We certainly liked ours a lot, La Pinta. It wasn't cheap. Metropolitan does offer heavy discounts on the Galapagos trips occasionally. Get on their email list. They provided excellent service, by the way.
If you look on tripadvisor you can find recommendations for a cheaper, smaller boat whose name escapes me at the moment, but you'll recognize it since it only takes about 14 passengers and it's the only one that is that small. Not deluxe, but as you'll see it has its fans and I would certainly take that trip rather than not go at all.
Be careful in Ecuador. Crime is a big problem.