A very often asked question here on the Bay Islands forum... search on the Cruise Ship forum as well.
The cruise ship contract operators seem to deliver a good product, on par with any similar situation.
The big discussion for most people is whether to do the AKR Dolphin Dive... or the snorkel Encounter. Most votes, by far, favor the Encounter.
The other "gotta dive" is the Shark Dive, also well discussed here in both the previously mentioned forums. It is not for the absolute noob, but for anyone who can follow directions and firmly hang onto a down line in potentially serious current, it's pretty much-so an easy deal.
A dive operator would be breaking local rules if he were to take you to the so-called "signature dive" of Mary's Place on your first and only dive day in Roatan. There are some who will slip you in, but is that the character of dive-op that you want to hang your survival on?
The general tally in most of these forums is to go with the provided operators. IF however you are considering spending a week at a resort or locale on a future trip for a Dive Vacation, why not consider contacting that opeartion and tell them that you wish to hire their services and have them arrange a day for you, door to door? It may cost you a few bucks extra, but if they handle it right, the diving as well as the cab driver- you picked a winner. If they go the extra distance and get it all set-up up for you~ you'll know you've picked a winner. Send out a few e-mails, see who responds correctly.