WELCOME TO THE DIS!!!!
We have gone three Junes now and the crowds are moderate and manageable. Three words: HOT HOT HUMID!!!
Get squeeze breezes to keep yourselves cool, take afternoon breaks at the hotel for dips in the pool to cool off (late afternoon terrible hot and humid and sometimes miserable), take advantage of fast passes if the lines are longer, if you have little ones, do extra magic hour for at least MK to get Fantasyland done with smaller crowds, and have a blast!!!!
If you are there the first week in June, avoid MK on June 7 because it is gay day there and it is crowded something terribly there!
Your son will love Disney Quest if he likes video games (boy, 9 years old? hmmmm). It may be his favorite spot. It is my son's favorite spot.
Have fun planning. You may want to head over to the Orlando hotels and attractions board to find info on your hotel and such. We have done Kennedy and it was okay. I was not that thrilled except for the Apollo set up and would have rather spend the day at Vero Beach, but that was just me, you know!
We love going at this time period; the summer crowds have not gotten into full swing and it is warm enough to really enjoy the water parks!