Pretty much anywhere in Thailand in September will be a bit hit-n-miss. The storms that hit the Andaman side in September will put paid to the Similan islands but there's still good diving in other places - as has been identified already. I am in Pattaya and of course would love you to come here however I am in complete agreement with the others that the marine life and viz will probably be a good deal better elsewhere. This time last year we had 25 metre viz on some days; the last week it rained for 5 days solid and viz is down to less than a metre. On the other hand, I was diving off Phi Phi in February and we had less than 1m on Hin Daeng and Hin Muang was filthy down to about 10m until by some bizarre twist we had perfect (albeit very dark!) viz - seriously, under that cloud of silt it was almost like night diving!! The liveaboard guys told us that just 4 days earlier the viz was over 30 metres! Diving - it's unpredictable!
In the gulf we have some great wrecks but the marine life is heavily depleted; the andaman side has lots more marine life (especially if you want to see some sharks), but the weather is more likely to hamper your diving. On the other hand, Storms in the Gulf (whilst not always as severe) will equally keep the boats at their moorings.
Wherever you choose to go, the main thing is, I hope you have fun!!