Depends where you are. On Phi Phi Island, the most reputable operations are considered Mosquito and White and Blue. We did our cert dives with Phi Phi Island village (a slice of heaven, check out www.travelforum.org/thailand),
where the instructors were as on the ball as any I have seen. PPIV is a resort away from the main town/crowds in Phi Phi (and the diving is a little more expensive)... but, it is a secluded gorgeous place with a gold palm PADI dive operation.
If you go to Phuket/Phi Phi, I would recommend Phi Phi over Phuket. If you stay in Phi Phi or Phuket, try to get a dive to Hing Maunge/Hin Daeng, one of the best dive sites in Thai waters. Trips leave sporadically as it requires a 4 people and a speed boat. Mosquito was going almost every day.
Both Mosquito and White and Blue have liveaboards that go to the Similan/Surins (worth the trip, but Richeleau is nice, but always 4 boats there, dive early morning).
Check out 'Dive Sites of Thailand' by Paul Lee. A great book available all over Thailand, I bought mine off Amazon.com
As for the Gulf, I haven't been there but the diving in the Andeman is considered to be substantially better. It depends on the time of the year as the Gulf and the Andeman have opposing monsoon season when diving halts.
Oooh, if you go to Phuket, also try and do some dives around Coral Island (or stay there a couple of nights, it is a private island and supposed to be very nice).
Have fun, great country.