If you go first thing in the morning, I would plan for a good 6 hours. After that, I have to be honest, I get tired of being inside when the beautiful Florida weather is just waiting for me when I step out the door. 6 hours would definitely give you time to see everything at least once and have a nice lunch at the counter service restaurant on one of the upper floors.
That being said, I'm sure you could spend longer, and with your son's ages. I'm sure they'll have a ball.
Like the previous poster said, your DH and yourself may feel like heading out to a nice lunch at Bongo's or Wolfgang Puck's, or perhaps doing a little shopping while your kids play at DisneyQuest. Then again, many on these boards wouldn't leave their kids alone (not trying to spark a debate here) which is understandable as well.
RyMickey