if you were to pick 2-3 stops to scuba at, which would you pick and why? any suggested dive companies to go with? any must see dives?
I have been to most of those locations on cruise itineraries but have not dived them. None of them are known for "must see dives" -- for that, choose an itinerary with Cozumel, Key West, or Grand Cayman.
Cruise ships are a great way of traveling with friends who may not share the same interests -- you can dive while they take the horseback trip, the shopping excursion, the rum tasting, or the Jeep Adventure (tm).
I've been on several dives while on a cruise trip, and I arranged everything myself with a local operator in advance rather than using either the cruise ship's shore excursion desk or an independent booking agent (like shoreexcursioneer.com). I ended up on some fantastic dives, but it was a lot of work to set up, and a lot of carrying my gear around. There are some destinations where it really is best to use the cruise ship's operator because of coordination factors and because the cruise ships do use high quality operators in some ports -- Belize used to be an example but that may have changed.
You're new at this and are at the point where any ocean dive is a good dive. You can have fun with the right mind set. The shore excursion operators as a group are going to be a little disorganized, there are going to be lots of people on the boat, most of the other divers will be inexperienced, and the sites will be easy, fun, but probably not world class. If you bring your own gear you'll be carrying it a long way.
Nearly all divers agree that cruise ships are not the best way to enjoy a dive. Whether diving is the best way to enjoy a cruise ship, on the other hand, is a question that everyone has to answer for themselves.