As an addendum to Daniel's post, here's a link to an itinerary that identifies some of the sites, like Mother Bethel AME Church, associated with the black experience in Philadelphia:
http://www.visitphilly.com/itinerari...ound-railroad/ The African-American Museum mentioned here is quite interesting, Germantown is architecturally and historically very important, and the food contributions to Philadelphian gastronomy cannot be missed.

The Boston African American National Historic Site on Beacon Hill is also well worth visiting
http://www.nps.gov/boaf/index.htm

There is also a Black Heritage Trail

Wow! So much great information! Again thanks! I think we are going to do Boston....one reason being the fact that it may be cooler due to it's being coastal! Philly will be our next trip!! Something to look forward to! Thanks for all the links! I am going to have fun planning! It's nice to know this is such a helpful group!

Coming a little late to the party... Both cities are great and you won't go wrong with either one, but wondering whether you've considered Washington DC? I took my friend from California and her husband on a whirlwind tour of the East Coast. She wanted to see Boston and New York. We added Philly since we'd lived there. I also suggested Washington to her. It turned out that her favorite by far was Washington DC. So many wonderful museums, monuments, green space areas, embassies, ethnic foods, government buildings, etc.