I can speak of experience of visiting Boston and planning Philadelphia (if not this year, then next) so I hope that helps to some degree.

Boston is a wonderful US city, very proud of its history and the Freedom Trail is a major higlight of any visit. You basically follow a painted route throughout the city, and can see all the sights that were involved in the American Independence. There are paid for walking tours but we've always just walked it ourselves, and with the help of a waking trail map have easily understood what each building is and how it played its part. It is fairly lengthy, and does go over the bridge into Cambridge as well for the USS Constitution and Bunker Hill Monument. It's a must do in my opinion.
Other highlights:-
Museums galore. Check out the Boston City Pass.
Fanueil Hall area and waterfront (whale watching, sightseeing cruises and Aquarium).
Prudential Center for amazing views around the city and some decent shopping and restaurants (Cheesecake Factory).
Beacon Hill area, stunning just to walk around.
Newbury Street, treelined major road with shops a plenty.
Boston Common, not quite Central Park but definitely worth a couple of hours wandering.
Cambridge, head over the river on the subway to Harvard College, Harvard Square and MIT.
Salem, a short hop on an Amtrak train takes you to this spooky place. A bit touristy, but worth it.
Fenway Park, Boston Red Sox ballpark, good luck with getting a ticket (if you go in season) but worth doing the tour anyway.
Fleet Center (now called something else I think), home to the Boston Celtics.
Samuel Adams Brewery Tour, a bit of a trek on the subway and quite small and short, but 4 free samples!!!!!
Just a few pointers there. We had 6 nights the first time and did quite a lot, last time we were there for 3 (at the end of our rtw trip) and still had new things to do. Great city, great transportation system and very efficient, good shopping, lots of decent restaurants and some good bars. Well worth a visit. One of my fave USA cities and I have been to quite a few now.

Philadelphia, I am only clued up on what I've read. Similar to Boston in there being lots of history involved in the city. The area where Independence Hall is and the Liberty Bell is often called "the most historic mile in the USA". Lots of nice squares, Rittenhouse is supposed to be lovely, and Penns Landing alongside the river, where you can do lots of nautical themed activities. Other things to note, the Art Museum (and those steps from Rocky), plenty of other museums as well, and of course Philly Cheesesteaks (two of the best outlets are right opposite each other and have loyal followings).
I'm sure there is plenty more to Philly than just that. Some comments I have had on other forums is that if you have seen one major USA city, then you have seen Philadelphia which although making sense to a degree I guess, seems a little weird when there are obviously different attractions in each city. Others have said it is amazing, up there with the likes of NY and Boston.

Finally, on the subject of transportation, how about Amtrak??? Despite an unfairly bad reputation in the USA, I think train travel is the way to go, especially when it isn't a major distance. Worth checking out anyway.

HTH.

A great post thanks very much for your trouble, great info, never thought of Amtrak will check that out.