cshannon, the answer isn't quite so easy. Much depends on your desires, but I'll at least get the ball rolling and give you some pros and cons at least for Lahaina Divers. I'm not a fan of Maui Dive Shop (mostly by reputation), but have no first hand experience to give you.
Lahaina Divers: Pros: Close to Kaanapali, departs out of Lahaina, later check-in time, big 46' Newton boats, less sea sickness, excellent whale watching on the way to Molokini and Lanai, geared toward the beginning diver, good service, discounts for booking multiple charters, excellent rental gear, groupings of 6-8 divers, snacks between dives, scheduled locations so you can plan where you're diving
Cons: Up to 24 divers on the boat, long boat rides to Molokini and Lanai, allow little independence of divers, boat is filled with Discover Scuba for afternoon charters, provide AL72 tanks
When we used to stay up in Kaanapali, the first couple of years we dove with Lahaina Divers, then we started getting up early and drove down to Kihei. It's about a 45 minute drive, so we had to leave by 5:30 to have time to stop for coffee and be at the ramp by 6:30am. IMO that's the only disadvantage of booking a charter out of Kihei if you're staying in Kaanapali. The advantages are that you have more dive ops to choose from, the boats are smaller with fewer divers, dive groups are typically 5-6 with a DM, there are still snacks on the boat, and you will not only dive Molokini, but likely some great S. Maui sites as well.
Personally, I think the boat ride from Lahaina to Molokini is fantastic. The views of the islands, the whale watching, and the smoothness of the big 46' Newtons makes it a very enjoyable trip. Plus I was always dry by the time I got back to Lahaina, which was nice.
The reason we stopped diving with Lahaina Divers was because we outgrew them. We're independent, advanced divers and prefer to dive with an operator that is geared toward the diving we want to do, but when we were beginners, they were great. However, when we go to Lanai, we still dive with Lahaina Divers, and just did an all day 4-tanker with them on Dec. 25.
Another option you could take if you want to dive some of the nice S. Maui sites is to book with Shaka Doug for shore diving. He starts a bit later (9am I think??) and his scuba bus has everything you could ever need for a fun day of diving. Maui Dreams also does shore diving in S. Maui, and they're excellent as well. I know there are shore diving guides up in W. Maui, I just don't know them.
If you're thinking of grabbing a charter out of Kihei, most recommended around here are: Ed Robinson's, Mike Severns, B&B, and I'll add Makena Coast Charters.