I've stayed at both places.
Banana Beach is much newer, with larger rooms (they're one-bedroom suites, with bedroom and kitchen/living area, about 600 sq. ft.) SunBreeze has motel-like rooms, large but still rooms, not suites. In that respect, Banana Beach is more upscale. The rooms on the water also have nicer views than anything at SunBreeze -- you're literally just feet from the sea.
Having said that, I like the SunBreeze pool better, and I personally prefer to be closer to town, so the SunBreeze location is my preference. However, the beach at Banana Beach is better than at SunBreeze or nearby, and some people would prefer to be a little away from things. Both are well-run, with good on-site management.
I'd go back to either, but I'd probably give the edge to Banana Beach.
Belize First Magazine http://www.turq.com/belizefirst/
Fun, Free & Easy Guide to Ambergris Caye http://www.turq.com/belizefirst/amcay/amberg.html