All the ways to get to Bonaire are listed here.
Info Bonaire - Airline Information and Connections
Also look at going thru Curacao and catching a puddle jumper over. Some of them are pretty small planes though. The timing works pretty well except that if you have an early return flight it can be an expensive overnight on Curacao since the first flight from Bonaire leaves after 8AM. The airport hotel in Curacao has been charitably described as a smoke-filled dump and the resort properties can run $100/nt or more. Plus a $30-40 cab ride to town. Insel also flies from MIA, Tiara Air from FLL. At one time someone flew from CLT also but that may've been DAE who recently went bankrupt.
If you want a full AI resort with all the amenities it's the Plaza Resort. Other resorts with dive operations and their own restaurant(s) included the Divi Flamingo, Harbour Village (upscale) Capt' Don's Habitat, Eden Beach resort or Buddy Dive. All have full resort amenities, including their own restaurant(s) and dive operation. Only the Plaza offers a full AI but Buddy's bundles breakfast. Due to ironshore on the north side, the only properties with a real beach are the Plaza, Harbour Village or Eden Beach - Divi has a small one also. Some of the others have sand over the ironshore but there's limited/no water access except via ladder.
Buddy's also offers a drive thru tank pickup at the street side of the property. Divi has the only (small) casino and is about the only resort that's walking distance to downtown.
Condo resorts with full amenities additionally include Sand Dollar Condos, Den Laman Condos and possibly one or two others - listed separately since both have dive operators and IIRC restaurants although I'm not sure of the recent status of Den Laman's. Den Laman has a tiny beach also.
Outside of these, some condo properties also have dive operators but may lack other amenities like food. Places like that would be Caribbean Club, BelMar condos, Windsock Apts. or Port Bonaire condos. PB is also in the flight path. If you find a nice condo/house for rent, chances are good they have an affiliation with a dive operator as well. Anything you find south of town in the Belnem area will require a five minute drive to the closest restaurants - either in south Willemstad or at the Plaza.
BelMar and Caribbean Club are also Buddy dive affiliated so you get use of the tank pickup. Dive Friends has a shop at Sand Dollar and another at Port Bonaire plus 3 more and you can exchange tanks at any of them.
hth,