Serving lunch for 3 y/os at 1:30 is too late I think. Did you put on the invite that you're serving lunch? If not then I would skip it as others suggested. Just do cake, I wouldn't even do snacks. You could add ice cream if you want to take up more time.
As far as games you could do a classic pin the tail on the donkey but do a pin the caboose on the train type thing. It would be easy to make out of poster board and construction paper. I would also search Oriental Trading Co or Michael's for some fun and easy crafts. I'm sure they having something train related! You could even get paper conductor hats (I'm betting the museum might have some) and the kids could decorate them with stickers. You may be able to buy fabric ones and the kids could use fabric markers on them. Doing a craft would take up a bit of time and be a fun take home. I also know that OTC has train whistles for cheap that would be a fun party favor.
I would think 30 mins for crafts, 10-20 minutes for presents depending on how many guests, 10-15 minutes for cake and ice cream...you're left with about 20-30 minutes you can do a game or explore the store. Things usually take longer than you expect anyway, so by the time kids trickle in and you clean everything up, you're pretty close to time. You could also take a couple of your son's favorite Thomas or other train stories and use those as back-up. You could also blow up one of the picture pages from a book (go to Kinko's) and play an I-Spy type game with them. You could hang it on the wall and kids could circle the item you ask them to look for.
Have fun! I love theme parties!!!!