There are over 60 identified dive sites around Bonaire. Most of them are along the bay of the west coast and around the uninhabited Klein Bonaire (“Little Bonaire”) which lies just off the western coast. Most of the sites off Bonaire are accessible by boat or via shore entry. Of course, you'll need a boat to reach the sites around Klein Bonaire.
Out of all the sites, I've picked out three to highlight: the wreck of the La Machaca, Bonaventure and Windsock.
If you're staying on a dive package at one of the resorts, then you may have one or two boat dives per day, with the option of shore dives afterwards. You can, if you wish, forego the dive packages with boat dives, rent a small pickup, and ‘self cater’ your dives where and when you wish. When using this option, be sure to heed advice you're sure to be given about not leaving valuables in the vehicle while diving.