I've been on several trips during the late September/October timeframe. The weather can be all over the place. Be aware that October can be extremely hot and humid - in 2009, it was well into the 90s every day and extremely humid. It can also be quite rainy - it's hurricane season! (We were at WDW for Hurricane Wilma in 2005). But you might also luck out and get very pleasant weather in October! You just never know - just be aware that it's possible that the weather can be very extreme either month.
Regarding crowds, I would say September is much better than October.
So if you're looking for low crowds and can tolerate heat and humidity well, I would pick September!
If the heat and humidity will be an issue, I'd go for late October.