Hi Sherri,
Without hesitation, I would say
Disney's Wilderness Lodge would be the best resort for a family of three with a young son. How do I know? Well, that's where we stayed with my son during his first visit to Walt Disney World when he was very young. The Wilderness Lodge is the least expensive resort in the Magic Kingdom area of the Walt Disney World Resort. It is a deluxe resort in every way, except the price. Because it is not on the monorail loop, it is significantly less expensive than the other three resorts in this area. Nonetheless, you can grab a quick four-minute (I timed it!) Disney bus from this resort to the Magic Kingdom. Or, if you're not in a hurry, you could set sail across Bay Lake for a delightful ride to the Magic Kingdom. Having such easy access to the Magic Kingdom is key for a family with such a small child.
Of course, I love Disney's Wilderness Lodge for a host of other reasons as well. The theming in this resort is exquisite. Just wait until you see the lobby of this spectacular hotel. I guarantee your jaw will hit the floor! The rustic decor, Western music playing softly in the lobby, the crickets chirping on property in the wee hours of the morning, the geyser that erupts hourly at the back of the resort grounds, the beautiful pool, the extensive daily kids' programs, ... I could give you a million reasons why this is the best resort for your family. We've stayed at a number of resorts since my son's first visit but, like his mother, he still considers Disney's Wilderness Lodge as his favorite. I guarantee your son (and his parents) will love it too!
Let me know if you have any additional questions with which I can help you.
Best wishes with your planning!
Jill