Here's another enthusiastic vote for Beachcomber Villas. It's worth mentioning that the they actually have 2 apartments (VRBO policy only permits them to advertise 1 apartment.) More info on apartment layout and amenities is available on the regular
Beachcomber Villas website.
We've stayed at BCV twice, for 3 weeks each stay, and have our next visit booked. Like you we prefer to cook in the apartment. We couldn't afford to stay on Bonaire for 3 weeks if we went out to eat every night. These apartments have everything you need to cook, including spices, foil, and paper towels etc. And if you require something else Leanne will have it for you before the words are hardly out of your mouth (gbf and ufcnp, you guys know exactly what I'm talking about!) There's even a Weber propane BBQ on the terrace, which is very rare for Bonaire rentals. Leanne is also an expert resource for shopping for food. Availability of many items on the island changes frequently. She can advise where to find the best meat or produce on any particular day.
For what it's worth, we've been visiting Bonaire regularly since 1996 and have stayed at 7 or 8 different properties. We've got a pretty good idea of what's available on Bonaire and are happy to look elsewhere when a more attractive opportunity presents itself. I frequently read reviews of rentals or resorts where people say "We've stayed there
every time we've visited the island, and we'd
never stay anywhere else." I appreciate the enthusiasm, but in general I don't trust those reviews because I think they lack perspective and objectivity. That's not how we roll. I spend way too much time between trips reading forums like this, and I'll be damned if I can find anything else quite like BCV. The reviews on their web page and VRBO site pretty much speak for themselves.
Our diving pace is similar to yours and I've worked the cost vs. value math previously from several angles. You can get a discount on a Dive Friends Bonaire dive package when booking it though Beachcomber Villas. It's currently $144 for 6 days of unlimited air or nitrox, which works out to $12/tank if you plan to dive twice a day. It's not advertised on the DFB website, but you can purchase a 15 tank card for $150 if you're staying 10 days or more on Bonaire. That's only $10/tank, but things get more complicated if you don't use all 15 tanks or if you use the card up before the end of your trip. There's no provision for ala carte tank rental with DFB. The only ala carte offering I've found on Bonaire is Carib Inn, where you pay $13/day for a full tank with $6 refills. The downside with Carib Inn is that there's only one location, it's on the south side of town, and you have to wait for them to refill your assigned tank. DFB has 5 locations, including one very close to BCV. You just swap your empty tank for a full one and away you go.
At the end of each day we look forward to enjoying cold drinks and conversation on the BCV oceanfront terrace as the sun sets over the ocean. As the BCV fans know, Tim & Leanne affectionately refer to this daily ritual as "sundowners". We've done this 42 times now, and it never gets old. Enjoy your trip to Bonaire.