Hi Merideth,
Great planning to take a trip before your son turns 3 since he won't be charged for admission to the parks!
If you don't mind the heat, visiting right after Labor Day Weekend can be a trip with very light crowds. In fact, I think you'll discover all of September to be lighter crowds. If you'd like to add a few extras to your trip.
Mickey's Not So Scary Halloween Party happens later in September and throughout October (the dates have not been released yet) and
Epcot International Food and Wine Festival is happening 9/28/2012 through 11/11/2012. October and the first weeks of November, too, have lighter crowds.
Also, in previous years free dining has been offered during the fall, which may also help you to determine when you'd like to visit. No offers are currently available, but if you keep checking the
Special Offers page and the
Disney Parks Blog you'll be able to be aware of possible discounts.
Overall, any of the times you mentioned should be great times to visit, so it may come down to if you'd like to do some extras and if you'd like to take advantage of the possibility of free dining.
Please let us know if we can help again; thank you for the question.