Check out options from JungleTomSafari - transportation only (land + boat), pkgs that include B&B or hotel + tours. Staying in the village itself is cheaper than at a hotel/lodge with water access only, as those lodges usually do pkgs with meals.
Also see http://casamarbella.tripod.com hotel (Daryl Loth is the owner), which some say is one of the best options for independ visits to Tortuguero. His Directions page is very useful, too - http://casamarbella.tripod.com/id6.html and contains more info on How to Get to Tortuguero.
You can take public transportation. Much cheaper!
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