For me the difference is what you want to see.
Cayman/Turks & Caicos is more bigger stuff, sharks, rays, tarpon etc. Also it's often deeper diving off spectacular vertical walls - some drop several thousand feet under you.
Bonaire is more macro/small stuff, frogfish, seahorses, lobster etc. You struggle to find a "wall" there. I would give the edge to Bonaire for sheer profusion of life though, lots of fish, live coral, fans, etc.
All three have turtles, we saw the most on Grand Cayman (it's their nat'l symbol and the turtle farm is there) But we also saw quite a few off West Caicos and Klein Bonaire. We saw the most sharks off the more remote T/C islands, West Caicos, French Cay - a 45min. ride from Provo on a faster day boat. I don't think you'll see a shark off Bonaire. Lots of Tarpon on Grand Cayman, both at Devils Grotto and Turtle Reef (both shore dives) You see them on Bonaire during the day and they'll hunt in your lights at night. Not counting Stingray City we saw more rays in the Turks/Caicos, there always seemed to be Stingrays laying around near the moorings. Although there were several flights of Eagle Rays at different sites off Grand Cayman.
The best mix might be Grand Cayman if you're willing to work at it. The boat operators will pick you up for spectacular wall diving, in the afternoons you can shore dive at almost a dozen sites and take a trip either by boat or drive to the East End for a different experience. Provo has no shore diving and the wall off Grand Turk is a longer swim out from what I was told by a local.
Bonaire of course is all shore diving. The only reason to get on a boat there is to dive Klein Bonaire or the few sites inaccessible/difficult from shore. We did 4 days of 2 tank boat dives our first trip, it was probably too much. One thing I personally experienced is there's often a sameness in Bonaire sites, same general topography, same fish, etc. Once my buddy asked me if we hadn't "dove this site" earlier in the week. I could make the same point about Curacao - we dove several sites there where I told my friends - by diving here you've just been to Bonaire.
One other aspect of Bonaire shore diving is that although (by a large margin) there's the most there, it's far from "effortless" Good boots and sure footing are required, some sites are a short hike from the parking area and many entries are difficult - over sharp ironshore with coral rubble underfoot in the surf line. At some you can look for breaks in the ironshore or previous divers may have piled up coral rubble indicating the best entry points. Get a sense of that by reviewing the site listings here:
http://www.shorediving.com/Earth/ABC/index.htm
And every site outside of town is unimproved with no facilities - in the afternoons many times we were the only ones there. I personally like that but you're on your own if something happens also. All the typical Cayman shore dives have facilities on-site. You also do a lot of tank hauling on Bonaire - the trucks are even set up for it, many have tank racks in the back.
One of the better Bonaire dives was Salt Pier. Neither Provo or GC have anything like that. Cayman has better wrecks, including the Kittiwake - a non-wreck cert required dive. And Stingray City - it's fun once.
Of the three, the best diving I've done is Turks/Caicos, followed by Grand Cayman then Bonaire. Land based, I would reverse T/C and Cayman. As mentioned above, I've only been to Provo also for two days b4/after a liveaboard.
For some idea of what to expect at each location - besides Youtube/Vimeo videos, here are some links:
http://www.bonairepanoramas.com/underwater.html
http://idiveglobal.com/locations/
http://www.awoosh.com/Saudio/Saudio_Turks&Caicos.html - thanks to Mike Southard for this. We did this two years ago.
If you're looking to stay somewhere to walk
to town - you'd probably need to stay in the expensive Grace Bay area on Provo. Downtown Grand Cayman is pretty much walking distance only from Sunset House - from Seven Mile Beach it's a short drive/bus ride south. There really isn't any resort properties in downtown Georgetown, they're mostly further north on SMB.
On Bonaire you'd likely need to stay at the Divi Flamingo to walk to town, many of the resorts are in "resort row" north of town or south near/past the airport/lagoon in Belnem. There's a few properties in town but they don't have the best house reefs - if any. The north resorts do, several are on named dive sites.
One other aspect to consider is that there is almost daily cruise traffic in Grand Cayman - often multiple ships. They all tender in right downtown. It's a good time to be someplace else. When the cruisers leave, some of downtown shuts down. Bonaire also gets cruise ships now, IDK the frequency. Since Kralendijk is much smaller, that must be a mess also. They moor at Town Pier - ruining what used to be a great dive - orange cup coral don't like being silted over by ship thrusters. In T/C the cruise port is on Grand Turk, never been there so IDK what that's like.
Most people going to Bonaire or Grand Cayman often try to do at least some cooking - typically requiring renting a condo instead of staying at a resort. Most resorts on Bonaire are condos. Food is expensive at any of them - it's part of living on a small island where everything is imported. Cayman is the only place where we made a concerted effort to at least cook part of the time. The CI$ is fixed at .80 to the US$ so you're 20% down b4 you arrive. It makes a difference, on Bonaire we had many meals that were around the same price as what you'd pay in a major U.S. city, on Cayman everything was noticeably higher. One advantage Cayman has is that the U.S. chains are there - for some of the quicker meals anyway. We only ate at 3 different places on Provo and I don't recall any of them being noticeably excessive.
Seven Mile Beach is nice, Grace Bay is georgeous. Bonaire is a desert island so it's unexpectedly hot, dry and in some places rockier than I expected. The south is really flat though, at some sites you can see divers at the next 3-4 sites farther down. If you're interested in any sort of nightlife besides sitting around resort bars, you'll want Grand Cayman or Provo. Provo has a (small) casino (or two) Bonaire has the barefoot casino at Divi Flamingo.
To answer your original question - I'll go back to Turks/Caicos. Grand Cayman also when I can talk my friends into it. Bonaire probably not until I've dove my way thru the Caribbean. Except for Cozumel, I've been to many of what are typically considered the "best" Caribbean dive locations - we do 1-2 weeks per year - somewhere different each time.
