With Continental starting up weekly direct flights from Houston Dec 16 for under $500, its a pretty easy call for a beginning diver.
Whereas Cozumel's signature dives are considered advanced (Palancar, Columbia, etc are all 80' to 100' drift dives), Bonaire is about easy access shore dives with little or no currents and perfect for all types of diving, especially training because the reef is so close to shore and in many places slopes gently from 25' to 130', so they can be dived at any profile with plenty of stuff to see above 50'. My wife and I did our OW referrals, AOW and several specialties there with Sanddollar (now Bonaire Dive and Adventure) and always had a comfortable situation due to the outstanding conditions (warm clear water with very little current)
As already mentioned, Plaza is nice, also Buddys and Sanddollar have great facilities and training programs.
My two cents is that while Cozumel still offers world class diving, it is rapidly losing its charm and getting more congested every time we go. When we were there last December, there were as many as 12 cruise ships in port one day and it was chaos downtown the entire trip. Prices have also risen drastically due to the influx of cruise ships.
Bonaire on the other hand, rarely sees a cruise ship, is safe to drive on and has perfectly safe tap water. Also, due to the fact that it is so far south, it does not get the chilly Winter nortes that sometimes blow out dive days in Cozumel. It does have a couple of pocket sized casinos, a hand full of bars and not much else in the way of night life (hey, thats what night dives are for)