Philadelphia

What's the difference between Philly and Boston? The streets in Philly are straight and set in a very practical grid pattern. Boston on the other hand is a maze of madness - just ask Roger. With a few other exceptions, that's pretty much where the differences end when considering either town for a peek into history.

Boston has Paul Revere, Philadelphia has Benjamin Franklin, who so happened to hail from Boston.
Philly has the Liberty Bell, Boston has "Old Iron Sides". My preference is to tour an actual ship that they actually rotate every so often, as opposed to a bell that doesn't ring anymore, but that's just me.

Both cities feature Duck Boat Tours that annoy the heck out of the locals, but they're so much fun! Speaking of Duck Boats, both cities sit on a waterfront. However, if you head due east from Boston and keep your bearings straight, eventually you'll hit Portugal. Head due east out of Philadelphia, you run smack dab into Camden, NJ. Once you get to the other side, be sure to look to the left of the "Benjamin Franklin Bridge" and notice the barbed-wire fencing of the "Riverfront State Prison". Note - prison, not state park, though it sounds so serene.
A few other similarities include a large population of registered Democrats. In fact, Philly is 80% democrats compared to 76% in Boston. Its that 4% difference that put Mitt Romney in as Governor of Massachusetts.

Of course, both cities have more than their fair share of very old cemeteries.
And of course, the presence of Ivy League universities. Philly has UPenn, Boston has Harvard. Okay, so technically Harvard is in Cambridge (don't ever accuse a Cambridge resident of being from Boston), but two of Harvard's campuses are located across the Charles River.

If you're afraid of falling ill while traveling, choose Boston. We have twice the number of doctors.

If you're into sports, okay, winning sports teams, come to Boston. Across Baseball, Hockey and Basketball, Philly has a paltry 6 championships, compared with Boston's whopping 29 championships. Notice I didn't include football? That's because the New England Patriots don't play in Boston.

All things considered they're both beautiful historic cities. I had a chance to travel to Philadelphia in March of 2008 for a conference. Personally, I'd avoid both cities until they've had a chance to thaw a bit more.
Ulimately, I suppose your decision could come down to your choice of foods. Allergic to shellfish? Avoid the Clam Chowder and go to Philly. Have a strong dislike of CheeseWhiz? Then avoid the Cheesesteak and head to Boston. Oh, and Philly also has this odd meat thing called "scrapple", if that has your curiousity up, then head to Philadelphia!

Just in case you're wondering, all above images were taken in Philadelphia!