S.K.
We went to Lancaster on vacation last year. My son was 5 1/2 at the time and my daughter was 8. If your son likes trains, he will love it there. My son loves trains, so a lot of what we did is train related. A few places that we saw:
Central Market: http://www.centralmarketlancaster.com/
Even if you don't buy anything, you should take a walk through the market. It really made me wish we were staying someplace with a kitchen instead of a regular hotel room. This is right in downtown Lancaster.
Strasburg Railroad: http://www.strasburgrailroad.com/
We went on a train ride and the Railroad Museum of Pennsylvania is across the street. They have a Day Out with Thomas multiple times a year here, but they also have regular train rides. We went on a regular train ride and both kids loved it (even my daughter who didn't want to go at first).
Choo Choo Barn: http://www.choochoobarn.com/
It's a really big working train layout and there is an admission fee. My son loved it and asked to go back every day. They even have a DVD of the layout available that my son watched for months. Plus there is a store next door that is full of Thomas merchandise. (For the rest of us, this was interesting, but if your son isn't into trains, skip it.)
National Toy Train Museum: http://www.nttmuseum.org/
There are lots and lots of toy trains on display and a number of working layouts.
Intercourse Pretzel Factory: http://www.intercoursepretzelfactory.com/
This was mentioned by someone else. Even if you don't do the tour, you might want to stop in for some pretzels.
Dutch Wonderland is also there. I have heard it's a lot of fun, but we skipped it. It looked a little young for my daughter's interests and the only thing there that would be of much interest to my son is the Thomas show, but we saw plenty of trains elsewhere.
Isaac's Famous Grilled Sandwiches: http://www.isaacsdeli.com/
In our quest for the best Amish style restaurant, we found Isaac's. We kept asking local people for a good Amish style restaurant and nobody would recommend one, but they all said that we should go to Isaac's which is a sandwich place. Finally after about 20 recommendations for it, we ate at the Isaac's in downtown Lancaster our last night. I'm not a big sandwich fan, but I was happy with my meal, my husband loved his sandwich, and my kids both ate their food. The service was great and they had a fish tank with a magnetic cleaning thing that kept my kids busy when they weren't eating. So now I have to recomment Isaac's.
And there is so much more to do. We also just spent time driving around the area and stopping at shops and other places that looked interesting.
Have fun!