It really depends on what you are interested in. If you are seriously into marine life, I'd highly recommend the Mike Severns operation. Pauline, who owns it, is co-author of one of the guides to marine life in the islands, and the guides will try to show you unusual endemic species. There are critter ID books on the boat, and the guides know how to figure out what you saw. That dive op tends to attract a more experienced clientele, but they also fill up very quickly.
If you would like to get out and do your dives and get back to do something else, B&B Scuba goes out earlier than anyone else, so you get to Molokini before the rush hour.
I would HIGHLY recommend making the effort to drive up to Lahaina one day to do the Mala Pier dive, either by day or with the Lahaina Divers boat at night. They combine the Carthaginian at dusk (tons of frogfish!) with the Mala Pier at night. It's my favorite Maui dive by day, but it ROCKS at night.