Any particular reason for those 3, or are they just places you've heard of? Bonaire & Cozumel are very popular dive destinations. A few questions that might help:
1.) Do you want to dive with a charter boat op. (take a boat out with a group, jump in, dive one tank, haul out, ride to another site, repeat, then head back to shore by mid-afternoon to do other things in the evening? If so, consider a charter boat - which I think could include any of your 3 plus Cozumel.
2.) Do you want to do 1.), but 4 or 5 dives/day, diving intensely and not a lot else? Consider a Live-Aboard.
3.) Do you want to mainly shore dive on your own schedule, drive around in a pickup, park on shore, walk in & out, without hanging with a group or having to meet a dive charter's schedule? Bonaire.
Here's a link to a trip report to give you some idea what it'd be like.
4.) When is this? Some people even wear wet suits in Bonaire; I dove in Cozumel in 76 degree water & didn't even feel particularly cool without one, and I really, really don't like wearing wet suits. The Bahamas are chillier in winter, from what I understand. If you normally wear a wet suit anyway, maybe you don't care. If not, maybe you do.
5.) Is seeing a shark really high on your agenda? If so, the Bahamas seems to be a go-to place to spot one (albeit don't expect a great white).
6.) Do you want to do much besides eat, sleep & dive? Belize has Mayan temple ruins to visit. You can privately book the same sorts of tours cruise ship visitors do. I did one in Belize; our group took a boat up the New River & did a jungle tour at Lamanai, and climbed atop 2 of the 3 Mayan temple ruins we visited (I was on a cruise, but you needn't be). I shopping or baking on the beach a big deal to either of you?
Richard.