Is a stay on Chaweng Beach in mid-September going to be too rainy? If not, where is a cool place to stay? If yes, where would a good alternative be in the region? I will be spending about a week in BKK before this and have another week to play with.

Koh samui September is a good choice, as you can see from below not so bad. if you do get some rain it would be 'cooling', use that time for spa/massage, relax.

Rainfall stats for Sep:

Bangkok 12.6
Chiang Mai 9.9
Mae Hong Son 7.8

Gulf of Thailand area:-

Koh Samui 7.5
Pattaya 7.2
Hua Hin 5.4

South Phuket/Krabi

Phuket 16.5

How many days would be good? I am wondering if I should hit up Hanoi for a few days or head back to BKK after my stay on the island?

September is my favorite month for Samui, generally lovely warm weather with the odd shower here & there. Around the end of Sept/early Oct the wet season will kick in but early to mid Sept is very nice. As for how long - play it by ear, Samui can be a great fun place, if you're having a ball then stick around, if for any reason you want to move on then do that.

Any suggestions for cool places to stay? I am looking for a place that has a cool party scene but is also very relaxing. I am 26 and do not want to be in a family atmosphere.

Chaweng is the busy area, lots of bars and clubs, sounds what you are looking for, there are so many places, depends on your budget.

I am hoping to spend no more than $130 per night. Also, I am interested in more of a contemporary feel than traditional.