September is statistically the rainiest month of the year on Phuket - but generally, as mentioned before, rain showers tend to be brief and then to clear - but not always.
I live on Phuket, but have vacationed on Bali. I like Phuket more - the touts are not so persistent, you feel far safer on the streets late a night, traffic seems safer, and the beaches tend to be cleaner. I was quite put off by watching toilet paper float by me during a swim in the sea - went in and never went back out.