Hi Jennifer,
The Fall is a perfect time of year to visit Disney with a toddler. The summer crowds have gone, and the weather quickly gets more moderate. As you can guess, September is the warmest of your three choices, and November the coolest. The crowds are generally moderate during all of the times you picked, so I would base my decision on what kind of weather you prefer. Even the end of September can boast highs in the upper 80s, while November generally has highs reaching into the high 70s/low 80s and it's a bit less humid. September can also be a bit rainy (not nearly as much as during the summer, but you can still have a passing afternoon storm). If I had to pick, I'd vote for October. Highs approach the mid 80s, lows are in the mid to high 60s, and, most importantly, the parks are all "decked out" for Halloween.
Mickey's Not So Scary Halloween Party is a wonderful, family-friendly way to get in the "trick-or-treating" mood with your little princess! In addition, Epcot has it's
International Food & Wine Festival in the Fall, where you can literally "eat your way" through Europe sampling each regions finest cuisine. Finally, October is still more than warm enough for enjoying your resort pool or the water parks.
Have a wonderful trip!
Tanya