Just got back from 2 weeks at Buddy Dive, trip report forthcoming, but I digress. Being a professional number cruncher and desk jockey, I wondered if the all inclusive price (transfer to/from airport, 1 bedroom condo, 6 boat dives, unlimited nitrox, truck rental and breakfast) was worth it. Long/short given all things equal we paid about the same to stay right on the water with the above amenities as we would had we rented a private home in a nice community and paid for everything separately. Actually Buddy Dive all inclusive had a slight edge - maybe $150 per person/week - and everything was coordinated for us. I didn't have to drive to boats, pick up rental car, etc. I love the convenience of being right on water, gear storage, 24 hr access to tanks.
I like boat dives for the access to Klein and some northern sites not accessible by land. I find a morning boat dive, 1 or 2 beach dives and a late afternoon/night dive right from resort dock works best for me. While I love beach diving, it gets messy and I get beat up. Interspersing boat and resort dives breaks it up and not quite so taxing on my old self!
Air to Bonaire is limited, regardless of where you are coming from.
If you are a first timer, consider doing the package thing from one of the bigger resorts, get the lay of the land and make a deterimination for future trips.
Dive Maven - did the 3 tank Park dive - great trip! Strongly suggest doing it.