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 [1], but itineraries that take in San Cristóbal [2] and/or Isabela [3] 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 [4], Seymour Norte [1], or Plazas (each costing a hefty $125 pp), while cheaper tours run to Floreana [5] 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.
Links:
[1] http://www.moon.com/destinations/ecuador-the-galapagos/galapagos-islands/santa-cruz-island
[2] http://www.moon.com/destinations/ecuador-the-galapagos/galapagos-islands/san-cristobal-island
[3] http://www.moon.com/destinations/ecuador-the-galapagos/galapagos-islands/isabela-island
[4] http://www.moon.com/destinations/ecuador-the-galapagos/galapagos-islands/santiago-island
[5] http://www.moon.com/destinations/ecuador-the-galapagos/galapagos-islands/floreana-island