There's not much to do at the airport. Especially in the AE terminal.
We took a cab to one of the big hotels in Isla Verde, asked the bellman to store our carry-on bags and ate lunch there. Isla Verde is one of the nicer resort areas and only about a mile and a half from the airport.
You could go to Old San Juan and back in 4hrs. directly from the airport. Cabs are easy to find downtown. But it's kind of shabby, mostly catering to the cruise ship tourists.
A lot of the big hotels in Isla Verde near the airport have casinos. Some have nice beaches also, but since we weren't guests, we were told that if we went out on the beach, security wouldn't let us back onto the grounds without a room key. Also you can't walk between hotels, they're all walled off and gated.
Check your luggage on arrival in Bonaire and when you get back home, there's a lot of theft from bags going through San Juan.
Also if you're on the AE puddle-jumper to Bonaire, be prepared to check your regulation sized carry-on at the aircraft. It's better to get anything you want out of the bag while still in terminal - it's easier to do it there than while standing in the propwash of the departing planes. Something they neglect to mention when you go through the gate and onto the tram that takes you to the plane.