We held our daughter's 3rd birthday at Choo Choo Bob's. We set the party to coincide with Storytime with Engineer Paul (storytimes are listed on the store's website). The storytime was great, with lots of train-themed songs and stories. The party room was big enough to contain all ten kids and parents, and is decorated to look like a little train depot complete with train mural inside the room.
The play area is stocked with play tables and mostly Thomas themed trains the kids are allowed to play with to their hearts content.
Just a note: the store can be pretty busy after a storytime. If you'd like a quieter experience, plan to go on a day when they don't have storytime or call to find the best times.
http://www.choochoobobs.com/
This is a train store, with everything from Thomas and Brio to train-themed party supplies, to model railroad parts, but it's set up so that families can come to play. There are several train tables set up, with benches for Mom or Dad to keep watch on the little engineers. In the front of the store are model setups that kids can run. There's even a birthday party room. This is a fun store that's inviting for families to come into.