J.,
You say your kids don't care for the history of Philly yet, but do you know that for sure? My playgroup started taking our kids on field trips, including historical homes in the area, like Hope Lodge, when they were 2, and my husband and I started including historical angles to our vacations and day trips from the time our kids were 3 1/2 or so, and they thrived in those environments, picking up facts/trivia, and being amazed with how much things were different back then. You may be surprised how much your kids enjoy these trips. There is so much that is kids-oriented in Philly, in the historical area, from the Once Upon a Nation storytelling benches to the impromptu plays in front of the Betsy Ross House (and a tour of the house, to see how people lived so differently back then), to the Liberty Bell, etc. Independence Hall requires a ticket (free, as I recall) and there often is a line, but check with the Visitors' Center, which also is a nice starting point. Your kids might love just walking around the area, seeing everyone in costume...Ben Frankln, everyday people, etc. I HIGHLY recommend it.
Then there's Valley Forge, which also has a trolley tour.
A great museum for kids is the Mercer Museum in Doylestown, http://www.mercermuseum.org/. My kids were about your kids' ages when we first went there. It is a quirky place, and it has some fun "challenges" just for kids. Doylestown also is a nice place to walk around, if your kids like that.
How about factories? Once upon a time we tried to get a factory tour in every time we went on our vacations out of town... We still like to do this if we can find a factory in the area. There's the Herr's Factory, there's QVC (which my son loved, but I haven't been to, so I don't know what it's like for a 3 yr old), and then there are various pretzel factories in the Lancaster area, and many factories in the York area. (We recently visited the Asher's Chocolate factory, which really wasn't much to see, but it's not too far from the Byer's Choice Doll Factory.) A factory wouldn't be an all-day trip, but you might be able to combine it with something else.
I have wanted to take my kids to Tuckerstown Seaport, but we haven't made it there yet, but I've heard great things about it.
We also started taking our kids to art museums when they were little, and galleries...even small, neighborhood ones, like the Michener Museum in Doylestown http://www.michenermuseum.org/events/, and the Woodmere in Chestnut Hill, http://www.woodmereartmuseum.org/.
There is the Castle Playground in Doylestown, which you could combine with the Michener or the Mercer museums, or with a stroll through the boro.
How about nature centers and the like? We used to go often to Morris Arboretum, and they have a fantastic outdoor railroad display. You can combine that with the Woodmere or with a stroll through Chestnut Hill, or with a visit to the nice playground in Chestnut Hill.
Good luck, and have fun with it!