That's deer season, you won't find anyone home in small town PA.

More to the point, you might find some iffy weather too, so listen closely to the weather report and watch the Weather Channel. Getting to and from places like Fallingwater could be a little dicey.
The incline in Johnstown could be a nice stop for a little one. The Flood Museum downtown is pretty interesting although your 4yo might understand just enough of what's being shown to ask some uncomfortable questions. Skip the National Historic Site at the dam site with a little one.
The Slinky Action Zone (no website last I looked) just south of Altoona is a good stop with a little one. It's kind of like a Chuck E Cheese but cleaner and age segregated. The railroad museum in Altoona has a bit more for the older people too.
Our little one climbed all the Thousand Steps (over 1100 rough stone steps) near Mount Union when she was 4. (And slept very nicely in the car afterwards.) Don't try this in ice, or other than on a Sunday in deer season because they are located on State Game Lands. Each step is different from the others (a key criterion when you're 4) and there's a great view on the top.
If the weather is nice getting out of the car in Boiling Springs is a nice stop. There's a little lake that you could probably walk around with a 4yo in about an hour. Nearby Carlisle has the U.S. Army Heritage Center trail between outdoor exhibits of such things as World War I trenches (a favorite of our kid and others who come along). They're more fun to toddle through if you don't read the interpretive signs to the little ones.
The State Museum in Harrisburg is good for a couple of hours with a little one, with a discovery room on the first floor. Again if the weather's OK, the Five Senses Gardens on Harrisburg's Capital Area Greenbelt is a good run around spot with a little one - even though all will be dormant by then, the stone maze and stream remain. It's located behind the Bass Pro Shop with lots of native fish in a big aquarium, and boats to climb over. Hershey's Chocolate World is another indoor option if the weather's not great. In downtown Hummelstown just west of Hershey, Toys on the Square has a great selection of the sort of toys the box stores skip, if your little one needs more diversion by then. The "Cocoa Castle" playground on PA 743 between US 322 and US 422 is a spot to run off some steam.
Just east of Lancaster the "Amish Farm and House" right on Route 30 offers some of the flavor without trying the attention span of a 4 yo too much.
I'm a believer that great art is inspiring to little ones, but I'm also thinking that taking a 4 yo to both Fallingwater and Kentuck Knob sounds like a real patience trying experience.
If you need a weather backup plan at Pittsburgh there is a nice children's museum on the North Side and the Carnegie Museum of Natural History is a great stop with a little one. IMO the Carnegie Science Center (across town from the natural history museum) is a little "old" for a 4 yo. A nice-day stop if it's on your way is the Cranberry Township playground just off US 19 north of "downtown" of Cranberry Twp.
Philadelphia's Please Touch Museum at its new location is a full day for a 4 yo. The building and one exhibit is left over from the Centennial Exposition to add some adult interest to the experience.