Philly's major food groups are cheesesteaks, soft pretzels, hoagies, roast pork sandwiches, pork roll (by way of Trenton), scrapple, water ice, and ice cream.
The common theme among these foods is that they're pretty much working class foods, so I'd say don't overthink it too much.
For breakfast (scrapple), you could check out Dutch Eating Place, a diner in Reading Terminal Market. The apple and blueberry fritters at Beiler's right around the corner are awesome too. Or you could hit up pretty much any spot that serves breakfast for a pork roll egg and cheese sandwich.
Cheesesteaks: I may get pelted with empties, but I say go to Pat's and Geno's. As far tourist traps go, this one isn't so bad. For as much debate as there is locally about the best and worst cheesesteaks, there really isn't a huge difference among the big spots. I say go have some fun with your son, try both, and decide which you like better so that you too can now be an asshole arguing on the internet. For the record, when doing the tourist thing my order is a "whiz wit" and Pat's 4 Life.
Soft pretzels: Buy them from a street vendor and put mustard on it. It's a pretzel, it won't blow your mind but it's a Philly staple. Edit: I should note that I don't mean a Super Pretzel brand pretzel here. The pretzel should look like an oblong 8 see linked image below.
Hoagies: Tons of chains here as well as pretty much every pizza shop. If you're going to seek a spot out, I'd recommend Dan's Fresh Meats.
Roast pork: This is the hipster answer to Philly's best sandwich. Top spots are Dinic's in the Reading Terminal Market or John's Roast Pork (they also have a really good cheesesteak). Get it with greens and sharp provolone. The greens will either be spinach or broccoli rabe (pronounced rob). I prefer the rabe but just a heads up that they're a little more bitter than spinach.
Ice cream: Another Reading Terminal Market spot, Basset's, basically invented Philadelphia style ice cream. Imagine what Breyers used to taste like and that's what you're getting there.
Water ice: Might be late in the season for most places, but Rita's should still be open and they have multiple locations. Stick to cherry, lemon, chocolate, or root beer and you'll be good. I like to get a gelati which is soft serve custard layered with water ice.
Like I said, this is what Philadelphians eat day in and day out but there's a pretty good food scene emerging outside of these to explore too. Let me know if you're looking for recs for finer dining or more ethnic options.