I won't mention the shop I work for here but I will say I'd recommend choosing a company that owns their own boat. Some of the dive operations here charter space on a boat so you may have several groups all doing their own thing on the boat with the captain only concerned with driving the boat.
Each day I see boats (like ours) who are masters of their own fate and have their own instructors and go out and do the dives as planned since there are not multiple groups trying to coordinate their dives. Most offer an equivalent to what we do: 2 Tank Shallow Reef Dive, Wreck and Reef Dive, Double Wreck Dive, Discover Scuba, etc.....