I was freelancing with New Way Diving shop for a while and they were good and friendly. Everything the poster above said is true. Especially the part of getting up early for the dives!
Early, right before the sunrise, you'll find yourself meeting other divers in front of the dive center while the nearby bar is still in its night groove with drunk people being their usual obnoxious themselves and bar girls chasing their last chances of picking up customers. I hated that.
Apart from this, everything else was well organized and professional. They are good.
On the other hand, you might be looking into what Big Blue has to offer as well. I suggest you ask for Rich! A great guy whom I met while working with him in Dive Point dive center and now he works for Big Blue. Knows the dive sites very well and is a good instructor. I don't personally know any other people in Big Blue, though.
Both dive centers are on Sairee beach which can be a little loud at night. Annoying if you're not the party type so beware.
In case you're looking for the best organized and most professional dive center on the island that still isn't a mass diver factory you might give the Dive Point center a try. They are in Mae Haad which is 15 minutes away walking distance from Sairee but much quieter at night.
If you feel best not standing out of the crowd, go for Buddha View! Many divers on the boat sometimes mean more fun for novice divers. The owner is a very nice guy who will make sure you have a great time diving on Koh Tao! Highly recommended.
Now, all the people I mentioned here are people I know personally, but I'm really giving you an honest opinion here. I know so many other people on the island as well and I haven't recommended those. It must mean something.
Hope this helps.