Since you're likely to be solo shore diving on Bonaire - I'd choose a dive op with multiple locations both north and south for ease of tank exchange. Unless you get the package deal with your on-site operator since every resort, apt. or condo complex has a deal with someone.
The operator with the most locations is
Dive Friends. Next is probably
WannaDive. Buddy Dive has three locations, two north and one south. The Buddy's location has a drive-thru tank pick-up also. The south location at BelMar is right near the road.
http://www.buddydive.com/
Really reasonable accommodations
not waterfront are the
Dive Hut in town or
Coco Palm Garden which is is south of town in Belnem so you'd need a car for either. Most dive packages bundle a truck also. Coco Palm is about a block from Bachelor's Beach - a decent dive.
Carib Inn has decent rates for being waterfront and Bruce Bowker is the go to guy to fix anything. There's also this place - IDK much about it except it's located a few 100' behind where we stay. Not waterfront but a short walk to it across the road. Really decent rates.
Bonaire Bed & Breakfast: Affordable Accommodation - Oasis Guesthouse Bonaire Hotel
Another option in town might be:
Bonaire · Blachi Koko Apartments - adjacent to Carib Inn so you could use their facilties. Also their package is with WannaDive. I think you'd like Bart at WannaDive - he's very involved in reef/turtle conservation efforts there. From BK you could walk to most of the downtown restaurants.
Karels Bar over water downtown is the divers bar not counting those at the dive resorts. Go to the Tuesday night Beach BBQ at
Coconut Crash at the Plaza Resort also. Good food and a lot of divers will be there. At least it used to be Tuesdays before Van Der Walk took over.
We like BelMar condos but they make less sense for a single price-wise. Most of the waterfront resorts have a single supplement also. Nothing is particularly far from the water on Bonaire - it's not a big island.
hth,