Hello Jayne and welcome to the Disney Parks Moms Panel!
My youngest daughter was four the first time we went to the Walt Disney World Resort and I can assure you that with planning your son with have a magical time. But, do you know who will have a better time? YOU! There is nothing better than seeing the Disney Parks through the eyes of a child. Every park has attractions designed for the young and young at heart. However, in my opinion, the Magic Kingdom is the best park for a child of your son's age and stature.
As for wait times, they are highly dependent on the time of year you go. There are a number of websites with fairly accurate crowd calendars. I would recommend either easywdw.com or touringplans.com. Also, if you are intent on reducing your wait times I suggest you get a copy of the book "The Unofficial Guide to Walt Disney World." It is filled with a ton of great information and includes touring plans designed to reduce your wait times.
Here is something else to consider- many of the attractions at the Magic Kingdom have amazing interactive waiting areas. Our favorite is
Dumbo the Flying Elephant. This attraction provides a buzzer much like you would receive at a restaurant while waiting for a table. Then, you and your little one can enjoy the immense indoor playground while waiting for your flight.
I hope this helps with your planning.
See ya real soon!
Anne