Coz will almost always be the cheapest as long as you find affordable airfare. Try flying to Cancun and crossing on the ferry to get cheaper fares.
Bonaire is mostl likely to be out of the path of most of the hurricanes that are a very real concern during that time of year. It is also likely to be the most expensive to fly to. Bonaire will offer you more flexibility in the diving days and length of stay, as well as offer the ability to shore dive at will. Downside to the shore diving is having to take anything of even nominal value with you lest it be stolen from your vehicle.
Little Cayman is the most laid back and relaxed of the three. It can be pricey to get there, and depending on where you stay, lodging can be pricey as well. Little Cayman Beach Resort is offering a 7 night package including airfare from Miami or Ft Lauderdale for $1495 from Sept. 4-Oct. 16. That includes all meals, 2 tanks a day (they usually run a 3rd single tank afternoon dive as well), and a night dive. It may be slightly more difficult to get a 4 day package because of air connections and such oriented towards 7 night stays, but if you are dead set on a shorter trip, you should be able to arrange something.
Little Cayman IMO has the best diving of the three with Bonaire probably in second narrowly ahead of Coz. All three are excellent places to dive, and others will give you wildly varying opinions of the relative placement of the three. Coz has the most nightlife, with Bonaire a fair ways behind, and Little Cayman having pretty much nothing to do besides dive.
It comes down to very different diving styles at each place. Coz is all drift diving (i.e. follow the leader with a DM and group) and has lots of pelagics (eagle rays, turtles, etc), but has suffered alot under the pressure of up to 7 cruise ships per day in port. There are walls that go down several hundred feet before levelling off.
Bonaire is very oriented towards shore diving, and has very healthy reef systems and great macro life, but very little in the way of larger creatures or pelagics. The water around Bonaire is not very deep, and the typical reef profile is more of a gentle slope, without many sheer walls like you would see in Coz or Little Cayman. Little Cayman is the king of Caribbean wall diving. It has walls that start in 30 feet of water and drop several thousand feet nearly vertically. It has a nice mix of pelagics and macro creatures, and the reefs are generally very healthy. The diving is almost exclusively from boats, and with generally very minimal current, most diving is from a moored boat, allowing divers to head out any direction they please instead of having to follow a DM to ensure being picked up by the boat at the end of the dive.
Any choice out of the three will almost certainly result in a great trip for you, but the most satisfying option will depend on what you want out of the dives and the destination.
