I think most people would agree that the best diving in Belize is around the atolls. If you are a serious diver and that's your chief interest, then you ought to look at staying at one of the atoll resorts. Manta and Lighthouse Reef Resort and a couple of others are excellent.
The downside is that there is nothing at these remote cayes but the resort -- no shops, no other restaurants or bars, nada. If you want a vacation as opposed to a dive trip, then Ambergris Caye or Placencia or Caulker or even Hopkins might be a better choice.
Belize First http://www.turq.com/belizefirst/