Cruises to the Galápagos are mostly nonexistent. Once you're here, you can choose from a wide range of boats for tours around the islands. You book these in Quito or Guayaquil or from abroad. Cheap economy vessels (typically converted fishing trawlers) are often poorly maintained and have guides with only a passing knowledge of English. Stick with tourist-class or luxury vessels, which generally offer three-, four-, and seven-night tours. The price tag per person for a double cabin on a three-night luxury-ship cruise can run $950–$1,600 in low season and $1050–$1,900 in high season. Off-peak rates usually apply from May 1 to June 14 and from September 1 to October 14. When you book, be sure to ask if the $100 park tax is included.
Boat tours mean dining and sleeping on board, with much of the sailing done at night to maximize time spent on the islands. Note that some guests may find it difficult to sleep if the boat is plying choppy waters. Most of these vessels employ multilingual naturalists who are knowledgeable in marine sciences. At least once a day you'll have an opportunity to swim or snorkel. If you want to dive, you should make arrangements beforehand, as it's not offered on all boats.
Storefront travel agencies in Quito and Guayaquil advertise "last-minute Galapagos tours", although there's never any guarantee you'll be able to find space if you wait that long. Quality varies widely with this option, too. If you can swing it, steep discounts can be had on a luxury cruises if you book last-minute with the tour operator and try to haggle a bit. This works best if you are already in Ecuador, last-minute international travel will likely negate any savings. You can also wait until you arrive on the islands and try to bargain for a cheaper boat fare. Operators of all vessel classes come to the airport selling last-minute tickets. The risk of doing this, however, is that you might not find an available boat, especially during peak seasons.