September is typically one of the slower months. Crowds do start to pick-up in October, and with the extension of the Food and Wine Festival this year (I believe it now starts on 10/1), I expect you would see moderate crowds. Probably lines in the 15-20 minute range.
Columbus Day doesn't have a HUGE impact on attendance, although it may spike a bit over the 3-day weekend.
The weather is still likely to be hot and humid. Not as bad as the summer months, but temps in the 90s are certainly realistic.
Last time we visited in late-September (2002), our biggest beef was with the precipitation. We had a half-day of rain for the first four days of our trip. Every one of those days it was raining by 4pm, and it kept coming on into the night. Fortunately we had a washer & dryer in our room. We were out of dry clothes by the second day.
Others will tell you that the September rains aren't that bad, so perhaps we just hit a rotten week. That period does fall within hurricane season. The rain we experienced was a direct result of a hurricane that cut up into the Gulf. So, just consider yourself forewarned.
