September would be slightly better. Warmer weather and minimal crowds as school is just back in session.
However, in November there is the FOod & Wine Fest at Epcot and that is a fun event to go to. The third week in November won't be as busy as the following week (week of Thanksgiving).
Either one will be good for crowds. September will be better, but expect more heat and humidity as well as a chance that a hurricane may hit. This doesn't majorly impact the parks, but if a hurricane crosses Florida, you can expect a lot of rain.
November will still be mild, Hurricane season ends Nov 1., but you may have slightly higher crowds, but still be on the lighter end of attendance.