We dive yearly in Kauai, and our favorite dive op is Fathom Five in Koloa. The go out of the Kukui Ula Harbor, which is convenient to most of the South shore area and close to lots of dive sites. If you go with them ask for Julie to be your guide. Be sure to request Sheraton Caverns site; it's one of our favorites.
We also dove with Explore Kauai Scuba (referenced on previous page) and had a great time. We dove the Mana Crack with them, which has the added benefit of getting a Na Pali coast tour during your surface interval. One downside is that they don't offer Nitrox, which would be useful on the West side dive sites they frequent (as they go out of a harbor on the Southwest side of the island).
If you want other advice on non-scuba things to do, send me a PM. We have a place there and have a PDF with info for guests that you might find helpful.