If there's just going to be the three of you - every cabin on the Kona Aggressor (except the quad) has a double bunk down and a single above it. Another thing that might be attractive is there's a non-stop, direct USAirways flight to Kona from LAX, PHX, and I'd guess SFO. With four of you maybe you could get the quad for your family. If you want to share with two teens...lol.
I second the Turks/Caicos Explorer recommendation also. It's good, deep wall diving. French Cay is some of the best diving I've done in the Caribbean, they do 2 days there. It's also usually cheaper than the Aggressor - runs the same route - several times they were at the next mooring over - and the boat itself is bigger - cabins with real beds instead of bunks. Your son(s) could share a downstairs cabin - still ensuite but with bunks/portholes - upstairs the cabins have big windows. It's also $200pp cheaper. Watch their specials page, sometimes they offer $4-500 off pp. on certain trips. Ours (late May) was $500 off.
Aggressor is all portholes due to the design of the boat. Explorer also has a third deck that the T/C Aggressor doesn't. It's a covered flybridge so there's tables/padded benches and they stock alcohol up there. One thing I liked about the Explorer is that most of the cabins are on the same level as the dining area/lounge with the dive deck behind it. It's a bigger boat (120') with a lot of private spaces. Food was really good also.
A good idea of what to expect - with thanks to Mike Southard:
http://www.awoosh.com/Saudio/Saudio_Turks&Caicos.html
From Phoenix on USAirways we were able to easily get to Provo by around 1PM - 1 connection. We were early so they dropped us off in Grace Bay for lunch/shopping for a couple of hours till the other guests arrived. It's $20pp for the van ride each way. Explorer is also going to hit you for a fuel surcharge and either boat has about $100 in port fees.
The "Roatan" Aggressor - actually it's the
Utila Aggressor also has 3 bunks per cabin. They start and end on Utila and mid-week they go over to Roatan for a few days. I personally think the diving off Utila is better than Roatan. In April you're at the tail end of the optimum season to see Whale Sharks also - but it's snorkel only - Honduras rules. It's a new boat also, IIRC they started using it last year.
You might want to factor in flight times and pricing to Utila also, it's not that easy to get to from our side of the country in one day. You have to be in San Pedro Sula - mainland Honduras - for a 3PM flight or on Roatan for a 3:30 charter flight to make the sailing. The flight to Utila also costs between $200-240 depending on origin.