Sleeping and eating on a boat is not for everybody, and if you are particularly prone to seasickness, consider a land-based itinerary. These are becoming increasingly common, both on organized tours and for independent travelers.
Most commonly you will be based in Santa Cruz , but itineraries that take in San Cristóbal  and/or Isabela  are also popular. Five-day tours start at about $600 pp, but savings can be had last-minute. If you want to do it yourself, you can usually find accommodations in the ports for as little as $20 pp per night.
As well as seeing sites on Santa Cruz, San Cristóbal, and Isabela, day tours run regularly from Santa Cruz to Bartolomé , Seymour Norte , or Plazas (each costing a hefty $125 pp), while cheaper tours run to Floreana  and Santa Fé ($75 pp). The other islands are out of bounds to day tours.
Doing it this way, you could easily spend less than $500 in five days, not including the flights. Note however that there may be no escaping seasickness even on land-based tours, because you will spend plenty of time on boats shuttling to and from the port, and they are generally smaller boats that roll around more.