Here is where we stayed
http://www.redcaboosemotel.com/ where you get to sleep in a real train caboose.
The Strasburg Railroad
http://www.strasburgrailroad.com/ was so much fun and the staff are all great with the kids
The Railroad Museum
http://www.rrmuseumpa.org/ where my toddler spent 2 and a half hours looking at trains!
The National Toy Train Museum
http://www.nttmuseum.org/ is literally directly next to the Red Caboose Motel.
And there was so much more we didn't go to see, like the Choo Choo Barn
http://www.choochoobarn.com/ which is a toy train exhibit. We didn't really explore any of the Pennsylvania Dutch/Amish Country either. Two year olds don't really care about horse and buggies if there are trains around.