I'd make my decision based on the two islands more than on any two specific hotels. Both Caulker and Ambergris can be great, but they tend to appeal to two different types of travelers (though the difference is gradually being erased as Caulker goes more upmarket).
A few things to keep in mind about the differences in the two islands:
* Caye Caulker is much smaller, in overall size, size of the town/village and in population.
* Ambergris Caye offers a far wider variety of restaurants, shops, groceries and upscale accommodations.
* Caulker has a far wider selection of budget and backpacker lodging, whereas Ambergris now has only a few budget places.
* Caulker is overall considerably cheaper -- especially in hotels, with the most expensive hotel only going for around US$100 in season. Snorkel and other trips may also be cheaper. Restaurant meals are somewhat similar in price, though on balance you can eat cheaper on Caulker and San Pedro has far more upmarket "splurge" places.
* While last year's beach improvement project did widen and improve much of the front side shoreline on Caulker, Ambergris Caye has far more beach frontage (north and south) and much better beaches than Caulker, though neither has world-class swimming beaches.
* There's more to do and see on and from Ambergris -- more tours, more nightlife, more options for just about everything, but then a lot of folks who prefer Caulker like it that way.
* A few things about the islands that may not be made clear in guidebooks or from Web ads:
-- A lot of the pipe water on Caulker smells awful, due to high sulphur content and brackish sources; also, I personally don't drink the water on Caulker, whereas I generally do on Ambergris.
-- Most hotels on Caulker do not have A/C and none that I can think of has a pool.
-- Due to its smaller population, Caulker has even more limited medical care available on island than does Ambergris. Basically, you'll need to go to Belize City for any treatment.
--Lan Sluder
Belize First Magazine
http://www.turq.com/belizefirst/