The only operation that goes to Moloka'i with regularity is Lahaina Divers. As for Lanai, you can choose between Lahaina Divers, Extended Horizons, and Hawaiian Rafting. Extended Horizons usually gets the nod around here for the more experienced diver. IMO the only advantage Lahaina Divers has is their big 46' Newton dive boats that provide a very smooth and easy crossing in sometimes rough waters.
IMO, if you're willing to drive to Maalaea Harbor to catch a boat, you might as well go all the way to the Kihei boat ramp. However, none of those boats go to Lanai or Moloka'i, so for S. Maui and Molokini charters go with Ed Robinson's, Mike Severns, or B&B (all departing from the Kihei boat ramp). One distinction Ed's outfit has are regularly scheduled charters geared specifically toward the more experienced diver, including two 3-tank charters per week.
The nice thing about Maui though is that there don't seem to be any *BAD* charter operators. It is all a matter of picking the one(s) that match your diving style, personality, wants, needs, etc.