Hey, we took our boys for the first time in July(2009), my oldest had just turned 5 and my youngest was 2&1/2. They loved it, there was plenty for them to do, plenty to see and go on. There are restrooms everywhere and baby centers throughout the parks. The only thing I would mention is that the toilets automatically flush, which can be scary for some kids, so take a little post it, put it over the sensor and when he is all done, you can remove it and let the toilet flush.
Take a stroller, I would recommend a double stroller since your oldest is 6, sometimes they need a rest too, since they still have little legs. A sit and stand would work well for you, or any double stroller you might have.
I truly think he will love it at 3 and there will be plenty for him to enjoy at the parks, they also have parent/child swaps, so you don't have to wait in the line twice. If the 3 yr old is too short for a ride (like splash mountain for example) you could get in line with the 6 yr old, ask for a parent swap ticket and then when you get off, your wife can go on it with the 6 yr old. There are several things to keep the 3 yr old entertained while waiting.
Parades are tons of fun for the kids, fireworks, character meet and greets, I think you will be surprised how much there is for him.
Wow...I didn't realize how much I would write! Sorry I wrote you a book!!
Have fun, September is a great time to visit!