I've been seriously disappointed and disturbed on Bonaire boat dives. I've asked to go when the boat is going to northern sites that can't be reached from shore. I've also gone on boats to Klein.
My experience was that in both cases the boat was loaded with cruise ship divers ≡ no buoyancy control, no consideration for the reef or other divers (I was bumped, kicked, run into, and pushed out of the way - same as the reef). Probably because of the type diver the boat went to heavily frequented sites (shore dives on the northern boat) that were pretty meh.
Certainly not worth the price of admission nor the aggrivation of watching reef destruction. There are far too many great shore dives to pay for this kind of diving. Caveat - maybe it was the dive operator or the cliientele that day or just my bad luck. Others mileage may vary.