Not sure if you already went, but if not, I definitely recommend checking out the PA State Museum in Harrisburg. Most of the museum isn't fun for kids, but they have a great area called the Curiosity Connection just for little kids. It's got lots of toys and activities, a pretend little farm, truck assembly line, boats and trains to climb on. Really, really fun, and so relaxing for mom, because the kids can't leave the area without a parent (it's walled off and only has one door that's kept shut).
Also, a little more expensive, but really cool if your kids are over 5 is the Whittaker Center for Science, also in Harrisburg. It's a huge science museum with several levels, an IMAX theatre, demonstrations, etc. Again, supercool.
Strasburg (about 45 minutes from Harrisburg) has a working steam railroad and a train museum that is really awesome. If you haven't seen those old steam trains up close before, it's really surreal. I think they run the trains year-round, and I'm sure they're heated in winter. It's just called The Strasburg Railroad, so should be easy to find online.