Just returned from a week on Bonaire.
Stayed at Sand Dollar and got a dive package from Bonaire Dive and Adventure next door. Both very satisfactory.
Would also recommend getting a unit at Bamboo Bali Bonaire (about $875/wk) and a scuba package (about $290, unlimited shore, 6 boat dives; free enriched air) from BDA. Bamboo Bali is across the road from Buddy's and the Habitat, one-quarter mile from BDA, so not on the shore, but very nice. Prefer the scuba package from BDA, but Buddy and Habitat packages comparable and fine.
Rent a Toyota pickup from Budget at the airport. About $228/ plus gas. Get your food at The Warehouse. Take some staples with you, and buy the rest of what two people need for $100 (Bonaire is on the USD as of January 1), without a lot of chips and alcohol.
Good and easy diving from BDA pier, day and night, and good boat dives and DMs, especially Annie and Travis. If you dive that way, you can use full-foot fins, and I guarantee you 15 different and rewarding dives in 5 days. Otherwise, take booties and open-heels, and be prepared for some challenging entries/exits. Oil Slick is perhaps the easiest, and that's a nice little jump.
Have a great trip. We did.