The two places on Bonaire that I have done the most night dives (more than all my other night nights, put together), have been:
#1, Bari Reef, off of Buddy Dive. ( off resort divers have always been welcome)
#2, 18 Palms, at the Plaza.
Both are great night dive sites.
Other great night dives we have enjoyed have been The Salt Pier, Windsock Beach, Windsock Resort, Capt Don's, and another access to Bari Reef, the rubble field just south on Den Laman ( although I believe this access is currently closed, as a new park is being created there).
Bonaire is also the only place that I have ever done a personal favorite of mine, a pre-dawn solo.
I absolutely love entering the ocean in the dark, when there is no one else there, and then watching the Reef wake up, and at some special point in the dive as the light grows stronger, seeing the nearly instantaneous "changing of the guard", when there is that moment at which, as if a factory whistle just blew, suddenly the water column is full of day time fish, that you only saw occasionally just seconds before.
It's also pretty cool to pass ",the first divers of the day", just heading out as you are exiting from your private dive.