Maybe none of the above?
If a beach is a priority plus a good house reef there's other options.
One could be Sand Dollar Condos. They're on Bari Reef just south of Buddy's which is one of the best known shore dive sites. There's a website for the complex but also look on vrbo.com as owners also list their units privately in the same complex. There's a pool and Dive Friends has a shop on-site. The nice thing about Dive Friends is they have 4 locations across the island for tank exchange. One downside at that location is you will have to drive 5mins. south to their Yellow Sub location for boat dives. And should drive 5mins.north to their location on the Cliff dive site which is just north of Habitat. Depending on your arrival - up to 4:00PM or so, DF will do the Marine Park orientation just for you on demand so you can start diving the next morning. Buddy's, Habitat etc. tend to schedule it around 9AM so by the time it's over plus the buoyancy check dive, the morning is gone..
Here's the little beach at Sand Dollar. It's not much.
http://www.bonairepros.com/images/uploads/accommodations/3 x 2 Den Laman 2-1.jpg But see the two silver dive trucks south of the Blue (Den Laman) condo building? This is what's there now:
https://www.facebook.com/cocobeachbonaire That has to be the best beach on Bonaire now.
My other suggestion might be the Plaza Resort south of town. It's maybe more expensive but is
all inclusive. And their Jr. Laguna Suites are niced sized rooms - I've been in one. Laguna looks out at the boat harbor, Oceanview is obvious. And balconies or patios. Plaza arguably has the nicest beach on Bonaire also. The two jetties in the top right corner are their dive site - 18 Palms. And Toucan Diving is on site for boat dives - nice thing about them is they do 2-3 boat dives day and have smaller boats so limit divers to 12. Toucan is located just off the lower right corner of the beach photo - they stage tanks at 18 Plams but you carry your gear from the lockers there. Or ask nice for a dive shop employee to run you over in their golf cart with tanks.
https://www.plazaresortbonaire.com/en
The Divi has the advantage of being walking distance to town for shops/restaurants. Also the resort just went thru a major renovation but I think the rooms are still small. I don't see how that could've been improved except maybe refreshed - they're low buildings right on the ironshore so nowhere to expand. Good views of the water though - you just can't get to it from your patio.
Everyone you mentioned offers 2-3 or maybe more boat dives per day. It's sort of hard to discern but on the Buddy's website look at the boats page - they mention it there. They do 2 morning dives and afternoon dives plus evening boat dives on demand - or maybe scheduled?. Also they do a 3-tank trip on occasion. But if it's to Slagbaai Park - probably too much for your new diver.
Habitat does 3 one tank dives per day. Usually that means they're diving Klein Bonaire across the channel or one of the north boat dives like Rappel and returning to change tanks/divers. If you want a beach though, cross Habitat and Buddy off your list - they don't have one. Buddy has some sand on top of the ironshore cliff but it's 20' or so above the water. You can see it in their website header photo. Habitat being just a little farther north is all ironshore - there's a ramp down to the dive dock but everything else is higher. Many of the Habitat villas don't see the water either - the bulk of the resort blocks it. Except the new ones (a couple years old) - IDK if you can specify one in your reservation.
One last "gotcha" is that the various resorts/shops have different access policies after hours. And some limit the amount of tanks you can exchange - often 2 per diver. So the sites with multiple pickup locations - Dive Friends, Buddy make that more convenient. Our condo key also got us into the public area of the dive shop so that was handy for night dives etc.
