I have only stayed at Captain Don's and Divi Flamingo and I would recommend either. I have also heard good things about Lions Dive, Buddy Dive, Plaza Resort and a few others that escape my brain.
Actually, as far as underwater life goes and water clarity...Cozumel wins hands down IMO, but Bonaire gives you something more important to me...FREEEEDOM!!!
If your not afraid of a little shore diving and are comfortable planning your own dives etc..then Bonaire tops Cozumel without a doubt. My buddy and I like to adhere to our own schedules, not a dive boats/DM's schedule. In Bonaire, if you want to wake up at 3am and do a night dive, there are tanks waiting for you..plain and simple.
Some people don't like the sometime physical portion of shore diving, yes it does take some work to get in and out of the water..nothing bad though...water is usually rougher in my pool than in Bonaire. Well I'll stop now because I could go on and on and on...