AA does not fly between the islands, Divi Divi and DAE are your only choices.
As for places to stay, there are many. Where depends mostly on what you need/want in a place. If you want upscale then Harbor Village or the Plaza are your better choices. If you want to be on the water but spend less Buddy Dive, Sand Dollar, Capt Dons and Eden Beach are several to look at. A new place Den Lamen is also on the water and worth a look. If being on the water is not way up on your "needs" list and a more modest place will do. Look at Golden Reef Inn. It's a couple of blocks off the water and nothing fancy but it is clean, safe and a good value. My personal choices are Buddy if I have a larger group going and GRI for 2. If I can get 2 or 3 couples in one condo the cost PPat Buddy comes down to a point that it's worth the extra money to be on the water. On the other hand if it's just a buddy and myself we stay at Golden Reef Inn. We can save nearly $500pp, being on the water is not worth that much to me.
As for dive shops, there are no bad ones on Bonaire, at least that I have heard about. I do have my favorites. If I am staying at Buddy, then I use the Buddy shop. They are a first class op and the staff are great. GRI and many other places use Wannadivebonaire. WDB is my other prefered shop. The owners are VERY customer oriented and go way out of their way to help the customer. Ya gotta love Bart and crew. I will dive with either of them. By the way, I think Liz at GRI will help arrange inter island air if you stay with her.
Where ever you stay, you will want a vehicle. Most places will include a truck in the package if you want one and you do. When compairing the cost of packages make sure what is included, you need to compair apples with apples. I would also suggest you NOT do any meal packages with the exception of breakfast. The resort restaurants are good but there are way too many great places to eat to be stuck at a resort.
As for what part of the island is best to dive, my preference is the nothern sites. The reef and dropoff are a little closer. On the other hand the double reefs of the southern end are good also. Heck dive them all.....at least that's my plan in a few days.