I did Cozumel and Roatan on a recent cruise and had fabulous dives in both places, so you are in for a treat.
In Cozumel, I dove with Aldora Divers and I highly recommend them. They were flexible and accommodated the cruise ship's schedule. I had to arrange my own transportation, but that was simple, just take a taxi. The dive experience was phenomenal. I was on a small launch with 4 other divers plus the DM. We dove with steel 120's and spent more than an hour on the bottom on both dives. Everyone on the boat agreed to let me pick the dive site and profile since I was the cruise ship passenger and had only one day in Coz and everyone else was there for the week. The DM Javier was very professional and made it safe and enjoyable.
In Roatan I dove with the ship's excursion, led by AKR (Anthony's Key Resort). The resort is beautiful and the staff are very professional. I did not have to think about anything as they pick us up and drop us off all on a carefully choreographed schedule. Unlike with my Cozumel dive I got to meet some other divers on my ship, for what that's worth. The downside is quite simply bottom time. We had a large group -- two busloads/two boats of about 16 divers each -- which can mean you spend a lot of time on entry and exit. They chum the waters so you get giant groupers and snappers to look at while you wait for loading and unloading of the cattle boat. People on SB and other boards say that ship's tour operator will take you to the closest reef even if it's lame, and we did just take a 5 minute boat ride to the reef, but I was pretty impressed with the dive sites themselves, although "We will be diving X today" was a stark contrast to the attitude in Cozumel where they asked me where I wanted to dive. We only spent about 40 and 45 minutes on the bottom during the two dives, respectively. I finished both dives with more than 1000 PSI (and returned to the ship with two hours to spare!).
The dive itself was so gorgeous and the 15 other divers on my boat were pretty well organized about gearing up and getting in, so I had a great time, but next time I would make arrangements with one of the several reputable dive ops on the island. They may give you cheaper, more personalized service with a longer bottom time. I have read positive reviews here on SB about Coconut Tree, Bananarama, and West End divers.
Good luck and have fun.