It depends on your budget, but you'll see the most via a cruise. Because a cruise is jam-packed, though, I'd recommend a hotel stay afterward to relax. I've written a number of articles on things to consider when choosing a cruise and on which island you should stay. I also have some hotel and cruise recommendations, but they're geared more toward the luxury market.
http://traveleater.net/2015/01/05/galapagos-islands-dont-wait-to-see-them/ almost 5 years ago
I always thought independent travel was the best option but for the Galapagos this is not true. After spending 4 days independent on San Cristobal and Santa Cruz and then a 6 day cruise I saw 500% more on the cruise. You can only see a minor proportion of the wildlife and islands without a guide and day trips are very expensive. If you fly to Santa Cruz you can get a last minute cruise there for as little as $500 for a week, however you will need to be flexible with dates. All cruises have guides on them and they are great, you will learn and see so much. about 4 years ago