As just one more data point:
I was in a similar situation as the original poster, on a RCI cruise a little over a year ago, as part of a mini-convention group, and I'm not a fan of large ship cruising. In Cozumel, I booked independently (fantastic experience with Scuba with Alison), but for Belize, based on what I had read on-line, I opted for the ship's dive excursion (to Turneffe Atoll).
As noted earlier in this thread, the big cruise ships all anchor quite far offshore for Belize City, necessitating tenders to get to shore. The biggest plus of using the cruise ship's dive excursion is getting off the boat first, directly to the dive boat, with no need for taking a tender into Belize City. Also, if there are any delays, with the cruise ship's excursion, the ship will wait for you. The operator we had was Hugh Parkey's Belize Dive Connection, and I think they handle all the cruise ship dive excursions. We got picked up directly by the dive boat... I think it was a 40-50' boat, with about 18 divers, 3 DMs, captain, and mate, iirc. With a big, fast boat, the rides were comfortable, and the boat didn't feel crowded. They took us from the cruise ship to their dive center on Spanish Look-Out Caye to pick up rental gear, tanks, etc., and from there to Turneffe Atoll.
They split us into three groups, with 1 DM for each. They said they normally split by ability, but since there was a bunch of us from the convention, they kept us together as a group of 7 (of widely varying experience), with the other divers in two other groups. We dove two sites: Mandy's Dandy and another site whose name I don't recall at the moment. The diving was very pleasant, with great viz and lots of corals and sponges, but I'm too inexperienced to say how it'd compare globally. It didn't strike me as that much different from my dives in Cozumel on the same trip, though. The DM sent the faster breathers up separately, letting the others have more bottom time, but I'm sure they had an overall time limit, too. After the dives, they took us directly back to the cruise ship, and we circled for a while to watch dolphins playing in our bow wave. The entire trip was an all-day affair.
People on Scubaboard seem to be pretty positive about Hugh Parkey's in general, and I was very happy overall: easy logistics, fast comfortable boat, not too crowded, friendly helpful crew, great diving. My only caveats are that the rental gear was very beat up (my buddy got a broken fin, my first reg set was missing a ziptie on the mouthpiece), and my DM was the only one of the 3 who seemed rather sullen. He also told me to abandon my buddy, saying that watching my buddy was his responsibility... (My semi-insta-buddy was a trained firefighter, so he was great at buddy skills, very situationally aware. However, he was an even newer diver than me and was having problems with his buoyancy, equalization, his broken fin, and being overweighted.) I don't recall there being any snacks provided, but there was a big cooler of drinking water.
The overall cost going through the cruise line was more than going independent: I think it was somewhere between $150-$200 for the two dives with all gear. But I was happy to have done that, avoid all hassles, and get away from the cruise ship masses for the day. If I'm in the same situation again, I wouldn't hesitate to do the same trip; but if I had a really long port call, though, I'd probably try one of the local operators, just for variety.
I hope that's helpful for someone...