As far as I know, Kohala Divers up at Kawaihae Harbor is the only operation running the upper Kohala coast. I used them a lot before and last visited them in March (just to say hello) and they seemed the same as I remember them from when Turner Lett was the active owner (he still "checks-in" from Florida occasionally). You can't miss 'em; just hang a left out of Mauna Kea Beach onto the main drag, take a left at the "T" intersection (turn right to go to Kamuela/Waimea), and drive about a half-mile or so until you see a smallish 2-story commercial building at a fork in the road, within sight of the harbor. They're on the lower level of shops at the far corner closest to the harbor.
In Kailua-Kona town itself, there're any number of outfits to choose from and I haven't heard of any real stinkers. Your experience really depends on the individual staff present at the moment. I'd suggest checking the local yellow pages and visiting the shops to get a feel for the op. Jack's is one of the bigger ops. I've used Kona Coast Divers a lot; they've relocated to Honokahau Harbor, outside of town. As far as specialties, there's DiveTek who apparently caters to tech-divers but they're new to me. BlueWater Hunters has a shop in the industrial area; they provide for freedivers (check them out anyway because freediver gear is different, I like their Kevlar-soled booties). Everybody I've mentioned have websites.
You may also consider shore diving. Kona's the perfect spot for it. Undoubtedly, the most popular is at Honaunau (Place/City of Refuge), about 30-40min south of Kailua-Kona (depending on traffic). Boat traffic there can get heavy so stay to the right side after entry. Dick Dresie ("Dick the Diver") has an interesting website that you should visit (I've seen his "Holey-Moley" long-nose butterfly numerous times. Some of them were in the black/dark-brown color. The "hole" appears to be a congenital defect; definitely not an injury despite first impressions.) Another poster on this board, Friscuba, may have more info.
My wife and I are going to be on The Big Island in February and We are looking for a top knotch Boat Dive Company. I actually got certified in The Big Island years ago. Anyway, we are staying up at The Mauna Kea so we want to do a couple dives up that way and a couple dives around Kona and of course the Manta night dive. Who should we book with?
