tkaelin may answer soon; I'll throw in a couple of recommendations.
Buddy Dive Resort has a nice setup, with piers and easy walk in/out via a couple of sets of steps. I prefer to enter and head north from their pier, past Captain Don's (which should also have a fine house reef; I haven't stayed there, but I've dove and like that stretch of reef), but heading south (toward Bari reef) was also good.
Sand Dollar Condo.s and Den Lamen are side-by-side, and if you stay there and dive with Dive Friends, you can use the on-site pier. Their house reef is Bari Reef, and it's quite a reputable one.
My Research Notes for Bonaire -
My Research Note For Bonaire
8 Day Trip Report: Sand Dollar, Dive Friends