There is no busy highway on Bonaire. In fact there isn't even a highway period. About the only place maybe not optimal for your needs is downtown as it does get a little crowded when the cruise ships dock at Town Pier. Once they leave downtown is very pleasant also. Nothing is really more than about 15mins. from anything - often closer.
I'm going to cheat and use vrbo.com for most of these. All meet your 3BR criteria - some are south of town in Belnem, others just north of downtown leading to a few in the Santa Barbara or Sabadeco area. I made a few brief comments on each.
Belnem Vacation Rental - VRBO 281562 - 3 BR Bonaire Villa, Oceanfront Luxury Villa / Beachhouse from $2995,- / Week - doesn't get much closer to the water than this. The dark water seen just off the dock is the Punt Vierkant dive site.
Boat dives from there would be at Buddy Dive at Belmar condos about 5mins. north. Or Dive Friends at Port Bonaire an additional couple of mins. Lastly Toucan Dive at the Plaza has a small fleet of smaller diver boats with nice ladders/swim steps - we've used them. 12max per boat but you're competing with their resort guests for spaces also.
This is the duplex villa to this one^.
Belnem Vacation Rental - VRBO 336665ha - 3 BR Bonaire Villa, Oceanfront Luxury Villa Beach House from $2995,- / Week
Both are probably 10mins. south of town. And there's no food options in Belnem. But it's quiet at night.
The 3BR condos at Belmar Condos as mentioned in my earlier post.
Belnem Vacation Rental - VRBO 582008 - 3 BR Bonaire Apartment, Bonaire Belmar Oceanfront Apartments Rent Direct from Owner
I've known about this one for a while. It's near/on Bachelors Beach so probably closest to Dive Friends at Port Bonaire. Also pretty close to the airport. Looks older.
Belnem Vacation Rental - VRBO 3668208ha - 3 BR Bonaire House, Cute Vacation Home with Sandy Beach
You may notice other rentals in that area. Most of them are in a small neighborhood a block or two inland. No views so I didn't mention them.
One of the condos at Port Bonaire. It's not a huge complex but I'm pretty sure jets taking off fly right over it still really low. Dive Friends is on-site there so that's one advantage.
Kralendijk Vacation Rental - VRBO 801064ha - 3 BR Bonaire Apartment, Port Bonaire (Sea View Apartment)
Now we're moving north of town. There are a few 3Br condos in town but mostly in larger complexes with shared amenities. Cruise ships dock downtown at Town Pier, I'd prefer to be somewhere else when they do - downtown Kralendijk is pretty small and narrow.
For food options there's van Den Tweel or Warehouse foods a little north of the airport. There's also a pavilion right downtown where locals sell fresh stuff - I'm pretty sure it was fruits/vegetables and fish. It's the small yellow greek temple (really) looking building waterfront.
This one is just north of downtown in a residential area. I believe Dive FriendsYellow Sub location is nearby.
Kralendijk Vacation Rental - VRBO 379124 - 3 BR Bonaire Villa, Private Oceanfront Beach Villa
This is one of the 3BR villas at Hamlet Oasis. It's the villa development north of the 4BR one I mentioned previously -
Kralendijk Vacation Rental - VRBO 3716206ha - 3 BR Bonaire Villa, Oceanfront Hamlet Villa 5, Near Diveshops, Restaurants, on the Water I'm pretty sure there's 2-3 other rentals along the same waterfront.
Now about 5mins north of that area to Santa Barbara.
Santa Barbara Vacation Rental - VRBO 945901ha - 3 BR Bonaire Villa, Oceanfront with Pool - know nothing about it.
Lastly Crown Ridge area gets some favorable reviews here on SB. Just a couple blocks farther north. Here's a couple of them:
Santa Barbara Vacation Rental - VRBO 331753ha - 3 BR Bonaire Villa, Luxury Oceanfront Home with Pool
Sunbelt Realty - Bonaire - Sabadeco rental
http://www.villacrownridge.com/
The expectation for all of the farther north rentals is that you'd find a boat operator you're comfortable with to drive to. Most are 5-10mins. away or less. Habitat, Buddy Dive, Dive Friends - all have larger boats with ladders/swim steps. Bonaire/Dive Adventure has smaller boats - larger panga style with side mount ladders. I don't know what Wanna Dive has at their Eden Beach (main) shop. I believe the Harbour Village operator is for their exclusive use - never see it mentioned here.
Sunbelt also lists other options.
Sunbelt Realty - Bonaire - vacation rentals
hth, have a good trip.