Just returned from Bonaire on Saturday. Man I love it there! Couple of my favorites:
Karpata - just a great dive overall. The soft corals on the top of the reef are packed with life.
Capt Don's House Reef (La Machaca) - probably the best macro life picture taking site on the island IMO (and in the O of many folks I've talked to down there)
Salt Pier - was pretty nice, large schools of fish hiding under there during the day, but not at night. Saw a ton of eels and a few octopus in the rubble. Don't know if I'd go out of my way to do it again though.
Candy Land - This and the other north side dives (Playa Funchi) are great as well.
Rappel - the top of the reef is always a treat with all the soft corals and fans waving in the surf.
If you really want a treat contact East Coast Diving -
Diving Bonaire on the wildside, Dive bonaire eastcoast and see the big 5. - and do a two tank morning dive with them. It's a bit more advanced diving from a 12 man zodiac purpose built for diving. You head out from the marina near Jibe City and do two drift dives. They stage everything in the marina to make it as easy as possible when you're out on the water. Back roll entry in waves, once everyone is in you drop down and drift along. At the prescribed PSI you kick out away from the reef for a safety stop and get picked up. Getting on the boat is super easy as they remove the center section of one of the inflatable tubes and drop a ladder in. Our first dive we saw ~8 turtles, eagle rays, big green morays, southern stingray. The second dive we dropped in south of tarpon hole and drifted south, saw 29 turtles, more eagle rays, HUGE sea fans and other soft corals. Two of the best dives I've done on Bonaire, without question.
I really like a lot of the Klien sites as well, Nearest Point, Mi Dushi, Knife, Rock Pile, Capt Don's - nice chill wall dives with a lot of fun stuff in the sand on the way back. So, don't thumb your nose at boat dives!!
We also did an outstanding florescent night dive with Flow Bonaire adventures -
http://www.flowbonaire.com/#/fluo-night-diving/ - using special florescent lights and yellow filters for your mask you get out and see how certain critters floresce under this light. Unlike anything else you'll ever do - it was a great experience. Also did the cave tour / snorkel with them - another awesome non-diving event that I would for sure do again. Flow is in the same building as BonPhoto just north of the entrance to Capt. Don's and Buddy Dive.