When divers talk about a destination in the Carib, Cozumel is ALWAYS near the top of the list. It is usually drift diving along the reefs there and very highly reguarded. Diving in Belize is usually off shore on the reef, a pretty good distance from Belize City. By unqualified, I'll state that I have never dived at either place. Will be going to Cozumel in the spring with my LDS.
As for diving from a cruise ship, I have done that on our last two cruises... First time on St. Croix and second time on three islands during a 10 day cruise with Celebrity, this past January. On each of those three islands, I did some reading on the internet and set up my own diving with vendors on the islands. On St. Maarten, the vendor I picked WAS the vendor that did business with the cruiseline and was very good. On Barbados and St. Thomas I picked a 'smaller' operator who provided a lot of bang for the buck and had an excellent time. Many of the dive operators that do business with the cruise lines, are real cattle boat operations and are not much fun. The one operator in St. Thomas, has a HUGE pontoon style boat, that handles about 50 divers. They pack you on, give you a safety briefing and a tank and take you out in the harbor for a 20 minute dive in the harbor. I stay away from them like the plague!
You might check the Rodales web site. There is a button there that says something like "where do you want to dive?" and you load in your distination and it will give you information on the operators at that location and comments from divers who have been diving with them. This is how I found my dive operators on Barbados and St. Thomas.
Good luck with the research and the diving!