Hi Marie,
Welcome back to Disney Parks Moms Panel. Thank you for visiting us again. My family loves taking fall vacations due to the cooler temperatures and lighter crowds. We also adore some of the special events taking place during the fall months.
Like you said, I am sure you will have a great time regardless when you take your magical adventure, but if I had to recommend one, I would suggest you visit during the later dates.
Epcot's International Food & Wine Festival takes place during both of the date ranges you mentioned, however, this generally only creates a noticeable crowd increase during the weekends. As long as you plan on visiting Epcot during a weekday, you shouldn't notice the increased foot traffic. The September - October dates are also part of The Twilight Zone Tower of Terror 10-Miler Weekend and with runDisney events being so widely popular, I believe you would notice an overall increase in crowds throughout the resort. Although the later dates do include Halloween, this holiday attracts more local attention and again, I do not believe the crowd increase will become overwhelming. (This is all completely based on opinion and is in no way a guarantee of crowd levels, but rather simply my recommendation.)
Speaking of Halloween, your son's might really enjoy
Mickey's Not-So-Scary Halloween Party. At this special event, they are able to dress up in costume and trick-or-treat in the Magic Kingdom. There is also a special fireworks show and parade. My kids love it! Tickets do sell out so buy them early if you plan on attending.
Enjoy your magical vacation,
Lauren