Here are some of the places to look at. All except for GRI are on the water - as expected you pay more for that.
All have an affiliated diveop onsite. And a dive dock or easy shore entry.
(roughly North -> South)
Northern dive resorts:
Capt. Don's Habitat
Buddy Dive
Sand Dollar condos - share Bonaire Dive/Adventure with Den Laman next door.
Den Laman condos
Eden Beach resort
Golden Reef Inn - affordable rooms/apts. a short distance from the water. dvrliz1 here owns it.
Harbour Village resort - posh.
The above are north of town - not walking distance.
"In town" dive resorts:
Divi Flamingo
Bruce Bowkers Carib Inn
above are walking distance to downtown.
Plaza Resort - a longish (mile+?) walk to downtown. It's a pretty sprawling resort, 18Palms divesite is on the north, diveop/boats are to the south. They move tanks there with a golf cart if that's any indication.
Condo resorts in Belnem, south of the airport:
BelMar condos - the other Buddy dive location - we stayed here, it's newer, quiet, great sunset views, decent house reef offshore but absolutely no beach it's on ironshore. It's a dive you'll do once on your BMP orientation dive then probably go elsewhere. It's not that bad but there's so much better 5mins. to the south. (The Hooker, Invisibles, Angel City, Salt Pier (if open) Vista Blue, etc.
Bellevue Beach condos - onsite dive services but no diveshop afaik. Divervince here rents his condo there. It would one I'd consider next time. google vinibu if interested
It's a quiet residential area but any food is a 5-10min. drive to town.
And there's at least a dozen more I'm forgetting.
The thing about Bonaire is that you'll mostly be driving to the better shoredives either north or south of these areas. Most of the really good dives are 5mins. south of Belnem or 5-15 mins. north of Habitat.
What's pretty convenient is the drive-thru tank pickup at Buddy Dive. Others that are almost as convenient (that I'm aware of) are at the Plaza, BelMar, or (I think) Wannadive at Eden Beach.
If you stay at BelMar, you can use the Buddy Dive facilities also. Personally Buddy was a little too spread out for me, esp. if you're in the north condos, they used to be a separate resort (Lion's Dive) so the Buddy diveshop is all the way across both resorts to the south. It's not a terribly long walk as they're both oriented perpendicular to the shore but something to consider. The better restaurant is on the other property also. Most people who stay there like Buddy's - some friends did.