Bonaire Boat Dives
No doubt the main draw of Bonaire is the shore diving, but there are many sites that you can get to only by boat. This is true for some of the dive sites on the north end of the island, but also for all of the dives sites around the smaller island of Klein Bonaire.
Many of the hotels and dive shops can arrange for boat dives, but not everyone does so don't assume it. For example, the shore dive guides I was with the first few days in Bonaire don't do boat dives. I'd recommend looking for an operator that limits the number of divers on the boat. There were just 4 divers plus a dive master on my dives and I believe the max allowed would've been 6 divers.
Based on two days of boat dives it seemed that it's highly likely that there'd be only one boat at a site at a time. The main drawback is you're tied to someone else's schedule and you probably won't be done with a two tank trip until around 2pm. In exchange for your time you'll be rewarded with visibility better than most shore dives, pretty calm water, and a few flying fish moving away from the boat.
Bon Bini na Kas
A good site to begin with as the diving starts in fairly shallow water and the best "views" of the reef start at just 25 feet down. When I was here I saw a green turtle amongst the many fish.
While not necessary to see a lot fish and coral, divers do have the option of descending to 100 feet. As usual, if the plan is to go deep then you probably want to make this your first dive.
This is one of the more popular boat dive sites. Skilled divers like to watch the waves crash into the cliff undercut from below.
Although you could go down to 120 feet, there's a lot to see in the shallows. In fact, the shallows are good enough that even snorkelers will be quite pleased.