We used to go during this time. Our schedule changed during the past few years so we are not visiting Labor Day week-end any more, but I will tell you our experiences from many years of vacationing at WDW during Labor Day Week-end. Saturdays are the busiest at MK. I did not find it the most crowded of all year, Easter holds that honor! LOL!! Usually Epcot and the other parks are not that bad. DTD is usually very crowded at nights as the locals go. Also the water parks can be crowded. IMHO the best day is Labor Day Monday. The times we have been there have been great, even the MK. I would just avoid MK on the Saturday and you should be fine.
HAVE FUN!!