On two trips to Cozumel I booked the diving thru Carnival. The dives were ok but not impressive. They tend to pick sights close to the docks (about 30 minutes away) and they treat you like novice divers.
That's pretty standard practice for cruise dive operations considering the kind of divers they generally get plus their need to keep to a defined schedule.
I can recommend
www.neptunesdivers.com in Grand Cayman. You can also shore dive there at Eden Rock. It is close enough to where the tenders dock in Georgetown that you could walk there. There are two nearby dive shops to rent tanks and other needed gear. You'll need a buddy because they won't rent tanks to a solo diver.
Some operators to check out for Cozumel:
www.scubawithalison.com
www.scubatony.com
www.eagleraydivers.com
You might also check with your wife and see if she'd be willing to go on a combo dive/snorkel trip. I'm pretty sure both Alison and Eagleray do combo trips.
Because the diving is good at all those stops, you might consider what you do to on the non-diving stops and chose your diving after you have made your other choices.
For example, the signature excursion in Grand Cayman is Stingray City. Most often this is done as a snorkel trip, but it can be dived as well.
Belize has lots of fun excursions, but logistics is tougher there because the ships have to anchor quite a ways off shore. If you do decide to dive there, the ship's excursion picks up directly from the ship which is way more convenient. If you want to see Mayan ruins, Belize is also the best stop to see them.
Roatan also has some shore diving. I think you can do some shore diving at Cocoview Resort and your wife can hang out there while you dive.
Finally, be sure to check out the message boards on
www.cruisecritic.com for ship and port of call specific questions. You can also find your sailing in the roll call section and meet others who will be on your cruise.