I've been to most of the diveresorts on that end of the island so here's my totally subjective opinion.
Buddy's/Lion's Dive is probably nicer(the best being Harbour Village) than Capt' Dons or Sand$. However Sand$ has a little strip of beach, Buddy's and Capt' Don's have none being perched on ironshore and low cliffs.
Actually Bonaire Dive/Adventures' (Sand$ house op) boat looked newer than Capt' Don's. But as you've figured out they're six-pack sized and would probably require a back roll. And all I saw was a ladder for getting back on board - doesn't mean they don't have a swimstep, I just don't remember seeing one.
All of the house reefs along there are similar. Buddy's is the Calabas reef site, Capt. Don's is Cliff/LaMachaca and Sand$'s is Bari Reef. I suggest you dive them all. Unless you're a guest, Capt' Don's charges $5pp to dive there, but you get to use their lockers and showers and it's really convenient, you gear up and walk about 40' to the divedock and fall in the water. If you're not staying there, pull into the circular drive by the lobby and drop your gear there and go park. It's a short walk down the path below the bar to the dive locker area. You don't see it until you get down the hill. For one dive, swim north to Cliff, it's about the only small vertical wall in that area and typically the current will help you back south to the exit.
One thing I will say about BD&A is that their boat came in while some of my group was still in the water. Although the captains on Bonaire are in my experience very careful and watch for divers in the water. And they were of course idling in at the time.
All three resorts have excellent facilities, storage, and easy entries off dive docks with stairs for exiting the water. I would agree with the previous poster that there's probably more to do at Buddy's or Capt' Don's but it's also going to be a more adult crowd - the bar at Capt' Don's in particular is pretty busy most afternoons. Sand$ seems to be more families.
The reason for boat diving is to get to sites otherwise inaccessible. Like Rappel, imho one of the best dives there. Also there's a lot to see out at Klein, turtles at Jerry's Reef, the only drift dive(that I'm aware of) at Hands Off etc. For us what worked the best was a couple days of morning two-tank boat dives then the rest of the week was spent shorediving.
Some of the regular shore entries can be tricky over the ironshore/coral rubble, esp. for the kids(if they've got 80's on their backs) So you might want to dive the house reefs more. For shore sites, I thought Angel City, Invisibles and Salt Pier were easy entries, at least they had a little sandy cove area that you could enter/exit at. Salt Pier is a DM escorted dive only, ask your DM or diveop to schedule it. And I wouldn't get in the water south of Salt Pier with the kids, especially in the afternoons, the currents can be ripping.
my .02