We researched the boats before we left, including getting the addresses of the companies that own the boats. They are almost all in Quito, and most are in the same neighborhood. We narrowed our list down to four boats, all first class. When we arrived in Quito we went to these places to negotiate. We had a price in mind (less than half the current Internet rate). We started with our number one choice and got the trip for less than the amount we had in mind. So, we only had to visit one tour office, although we did have to wait a day for them to confirm that the cabin was still available.
In order for this to work, you need to have a little flexibility around your departure date. We were spending a month in Ecuador and had about a one-week window of viable departure dates for the Galapagos. I also spent many hours researching boats before we left to arrive at the short list of boats we wanted. Bottom line, we got a great deal on a one week trip on Creter Tours' Treasure of Galapagos. If you don't have date flexibility, I think there is some risk that you won't be able to get the trip you want with this approach. If you can schedule around your booking, it's true that you can save over 50% by booking at the last minute, particularly if you cut out the travel agency and book directly with the company that owns the boat. Many of these companies also happen to be tour companies (like Creter tours).
On an unrelated, note, the quality of your naturalist guide will have a large impact on the quality of your trip. If you can, find out which guide you will have and check out their reviews as well. We had a last minute switch on our boat (the original guide got sick) and the substitute was something of a disappointment.