When we were on Bonaire in March we stayed at Sand Dollar and rented tanks from Buddy's. That worked out great for us -- the drive through tank pick up was very efficient and we stored our gear in their locked room at night.
We had an unpleasant experience with one of the owners of the BDA facility one day when we dove Bari Reef. We entered from the Sand Dollar beach next to the dock, never used any of their facilities at any time but did make the mistake of parking our truck in their parking lot way out by the road. We walked down their driveway and then back onto the Sand Dollar property before walking the rest of the way to the beach. We didn't realize we were doing anything wrong, but that was enough to prompt a rather rude encounter with one of the BDA owners. Needless to say, I will never give them any of my business.
On the other hand, Fish Eye Photo, the underwater photo shop on the premises, was terrific.
So my recommendation is:
Sand Dollar for lodging,
Buddy's for diving, and
Fish Eye Photo for photography.
Cheers!