I would think that the last week of September will be the least crowded time this year.
1. Most schools have not been back in session for long so i think parents would be least likely to take their kids out for a week so early in the school year.
2. Yup, its hurricane season, but then again Hurricane Season starts in June and is not OFFICIALLY over until like December 3(?)
3. October 1 is the start of the new promotion for Disney, i'm sure there will be a big push to get people to visit at this time, not to mention all the press for the start of this Promotion.
4.. At the end of September you can still catch the beginning of the Food & wine Festival but will miss the
MNSSHP at MK but will also miss the local crowds that visit for weekend to attend MNSSHP
5. Columbus day is October 9 this year - which may also increase crowds the beginning of October.
Weather wise i dont think there would be much difference from the end of September to the beginning of October. Price wise it will be a little cheaper in september than October (goes for airline tickets also). I think crowds would be a little lighter in September than in October.
Disney has an excellent reputation of keeping their guess as save as possible during inclement weather emergencies, we were at WDW during Hurricane Wilma last October and the staff was great. It started to hit the area at approximately 7pm at which time the parks were cleared. It was requested we stay at our resorts until 2pm the following day at which time the parks started to reopen and transportation went back on line.
hope you have a great trip whichever time you decide to go.