I think your 3 year old will have a blast.
Recommend you go to Dutch Wonderland early when it's less crowded, sunny and hot. Remember the sun screen, hats, and possibly a parasol if you're holding a baby while he's on the rides.
If he's a train buff, there are some awesome attractions:
--Strasburg Railroad where you can ride a train:
http://www.strasburgrailroad.com/
--RR Museum of PA (across the street from the station):
http://www.rrmuseumpa.org/
You can see cars all throughout the history of trains; there's also a back room where you can try to run an electric train
--Choo Choo Barn (name sounds tacky, but it is a cute minature train display):
http://www.choochoobarn.com/
--Minature Train Museum:
http://www.nttmuseum.org/visitors/index.htm
I would pace yourselves and not try to everything.