It depends on what you want and how much money you want to spend.
Belize has a barrier reef where pretty much all the diving happens. Staying on one of the Cayes puts you right in the action - you're 5-20 minutes from any dive site by boat. Pros - you're right there! And the local beer (Belikin) is delicious! And you get to drive a golf cart if you want! Cons - it's all boat diving, which can get spendy, plus you're on an island, which can get spendy. Farther south on the coast (near Placencia) is reportedly way cheaper, but you're still boat diving, and since you're farther away from the reef, it's a much longer trip.
But the diving is lovely, the people are lovely, and the food is delicious. Plus the Mayan ruins make for great day trips.
For Honduras - I've only stayed at Cocoview, which is an all-inclusive dive resort on Roatan. Pros: 4 boat dives a day plus unlimited shore diving whenever you want, 24/7. It's set up to dive dive dive, and then dive some more. Price was reasonable IMO. Diving was lovely. Cons: there's not much to do if you don't dive, as the resort is on it's own small "island" (only nominally separated from the mainland, but still), the accommodations are nice but not luxurious, and take some snacks - they provide 3 meals a day that are buffet style and plentiful, but it's a loooong time between lunch and dinner.
Oh, and for the month of July, REEF does a fish survey marathon with classes and whatnot, if you're into that sort of thing.
Utila is another island off the coast of Honduras where the big draw is whale sharks in whale shark season. So..whale sharks! But I've not been there, so I can't speak much to that location.
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