Yes, it's going to be not only hot, but humid too. I'll be there 9/6-13 and am not really a heat person, in fact, I used to live in Oregon and I daydream about spending summers on the OR coast...but--if I can take it, you'll be fine. We went last year over labor day as well. We used the misting things, wet paper towels, had a fan on the stroller for the 2yo. There are a lot of places to escape the heat for a little break--try to hit Fantasy Land in MK early in the morning or in the evening, that seems to be a hot spot esp as crowded as it gets. Go to things like Ellen's Energy Adventure(EP), Tiki Bird show(MK), ride the TTA(MK)... hit AK early and leave when the heat really gets bad.
Honestly, the crowds were so bearable that it made up for the heat!! That's what we are hoping for again this year. And hopefully you have your ADR's all planned out which is another great break in a cool spot.
Do bring a cover for the stroller and get in the habit of covering it even if it doesn't look like rain, it rains about every day and with little warning at times.
Also--you can ask for a glass of ice water at any concession stand--the water is a little funky tasting but I got used to it, experienced no adverse effects from it and loved having the ice to suck on.
Try to keep your son drinking, eating grapes, apple slices, ice pops--that's my plan anyway.
Have a wonderful time!!!!!