Hi. I went with Klein Tours to the Galapagos in winter, 2008. I was on the Legend. I had my doubts- my traveling companion had chosen the trip and then asked me if I wanted to join in. I had never done a cruise before. I ended up being very impressed the Klein. The guides were first-rate, and I loved the crew. Even though it was a bigger boat, it didn't feel that way. The other passengers were interesting and fun.
We used a budget travel agent here in the U.S. She demanded we pay in full in advance with a cashier's check. (she wouldn't accept credit cards because of the fees) I was half-convinced we were getting scammed, but everything turned out fine.
I did talk to Klein directly about booking an extra day trip out of Quito. Their price was higher than a competitor, so we took the competitor's day trip to Otavalo. (Klein supplied an individual guide, while it's competitor had a chartered bus-trip.)
I would book with them and pay in advance again. But I would price-check any add-ons out of Quito.
Hope this helps!