I have been to Bonaire 4 times, not of the others. I had 2 dives in Costa Maya, and 2 in Cozumel (Palancar Gardens & Santa Rosa; the second was much better), so I've got to visit the 'Meso-American Reef,' which I suspect would be similar to Belize. This experience is anecdotal.
1.) In Bonaire, 4 trips (about 65 dives total, I think), I've seen 2 eagle rays, neither let me close.
2.) At Santa Rosa in Cozumel, after we back-rolled in & were waiting to get moving, a big eagle ray swam right under us, close.
3.) In Bonaire I have seen a few grouper of size (like 3 feet or so), not real regularly (I'm not counting graysbys and conies). At Santa Rosa, a big black grouper (it wasn't black, but that's the species) swam up almost touching distance and followed us awhile (I think it's used to divers feeding it).
4.) On the first dive at Cozumel, by buddy pointed out a yellow stingray. On the second, our guide pointed out a southern stingray.
In Cozumel, we dove with Living Underwater, a well-regarded operator who had 120 cf steel tanks. I'm a big guy, and air hog, and I LOVE 120 cf steel tanks! Dove over an hour & 15 minutes! Yay-us!!! If you've air hogs along, see what your dive op.s can offer.
If you go to Bonaire, hit Hilma Hooker, so if you see nothing else big, you'll at least see some tarpon.
Any chance you could stay over a week? If so, the land adventures like the Mayan ruins might be a big draw for Belize.
Richard.