The glory of Bonaire is shore diving. Easy diving when, where, however often you want to without a boat or guide. Driving a manual transmission truck with gear loaded in back around the west coast perimeter, stopping at a site marked with a yellow rock, pulling off road onto dead coral rubble, backing up facing the ocean, getting out, gearing up walking in without fins on, wading out to 4 feet deep, putting fins on, swimming out, then around 20 feet deep or more, there's a roughly 30 to 45 degree (guessing) 'hill' sloping down to the sand well over 100 feet deep. On that hill are abundant coral formations, and varied fish, mostly not big stuff but you might see a tarpon, barracuda, etc... You head down to a target depth, turn & swim perpendicular to shore, reach your turn pressure, and come back. Drive down the road and repeat. 2 To 4 dives/day, 5 or 6 if you're hard core.
It can be done differently and there is boat diving, but I think I laid out the standard. With shore diving, there's no boat staff to tip, but food costs can be substantial. Figure on a $70+ tank of gas late week for that truck.
I've been to Bonaire 7 times, Key Largo once. Loved both. Key Largo reef diving is mostly shallow; Bonaire diving can be 30 feet, 60 feet, 80 feet, etc..., at the same reef site, up to you. Viz. was better than Key Largo. With minimal current & high viz., wreck diving the Hilma Hooker is significantly easier than going up & down a barnacle clad mooring line in current to the Spiegel Grove and the Duane, plus you get a nice reef, but not Goliath Grouper.
I have not been to Little Cayman. From forum postings, Little Cayman Beach Resort is well-liked, the main place I'd research, and consider whether it's all inclusive. I believe Little Cayman is mainly boat diving.
Richard.
P.S.: What I saw in Key Largo that I didn't in Bonaire: Goliath Grouper, Porkfish, Atlantic Spadefish, Hogfish (Spanish Hogfish in both), 2 Nassau Grouper, a # of Black Grouper, Reef Sharks, Nurse Sharks, a few big Stingrays (at least one was a Ridgeback; in 7 1-week trips to Bonaire I saw one big brown stingray in Bonaire, a few eagle rays, never got near them; I did 20 dives in 5 days in Key Largo). I saw more big barracuda in Key Largo.
Bonaire had Tiger Grouper, a lot more sand divers, and I have seen a couple of sea horses and a frogfish there (all shown to me) and 2 star fish (one on the east side). I saw octopi and reef squid in Bonaire. I know Key Largo has some of the things I just didn't see there.