The boat is cheap. Here's a schedule and pricing. Note the prices are in Belize dollars -- and you get almost 2 Belize dollars for 1 US dollar.

http://www.cayecaulkerwatertaxi.com/pricing.html

From a first timer perspective, flying to Caulker seems a little silly, since it's only a 45 minute boat ride. Flying to Ambergris (1 1/2 hour boat ride) just seems unnecessary. It's apparently a 20 minute and $25 taxi ride to get to the boat dock from BZE. I understand there are also some flight savings leaving from the local airport instead of the int'l airport, but if you're going to take the time to switch airports, it seems like you might as well take the boat.

In booking my AA flight times, I thought I'd avoid the 6:00 am departure for a slightly more civilized 7:30 am departure -- especially since it only arrives 1 hour later. The problem, however, is that the later 3:30 arrival might miss the last boat to Ambergris (there's a 5:30 boat to Caulker, so no problems). Just something to keep in mind. If you're trying to get to Ambergris from the 3:30 flight without spending your first night on the mainland, you might have to fly.