As WetRat and Al posted above nice dive shops in the S. Maui area are Maui Dreams and B&B. I've had good experiences with both. Friendly, helpful divers that just happen to be running a dive shop.
Although your thread title says dive shops, since you are just coming for a honeymoon I assume you really want info on dive charters or dive operators.
In S. Maui (Kihei, Wailea, Makena) my favorite dive ops are Mike Severns (great for fish nerds), and Ed Robinsons. B&B is also popular boat. The typical trip is one dive at Molokini followed by a dive somewhere off S. Maui. Boats depart from Kihei boat ramp in the south part of Kihei.
In West Maui (Lahaina, Kaanapali, Kahana, Napili, etc.), Extended Horizons is my favorite dive op. They depart from Mala ramp in Lahaina and usually do two dives off the south side of Lanai. Lahaina Divers runs bigger boats out of Lahaina harbor and would be better for someone prone to seasickness. They have boats going to both Lahaina and to Molokini.
Mike Severns, Ed Robinson's, B&B, and Extended Horizons all take 12 customers in two DM-led groups of 6. Lahaina Divers is IIRC, has 24 passenger boat. The other mega-operator, Maui Dive Shop has several different sized boats. The 12 px boats mentioned above are consistently good since they have either the owner or long time employees onboard. Lahaina Diver and Maui Dive Shop vary more from day to day.