Richard: I have given to many tours of Philly to count ( Ask Nick about his one hour layover at PHL tour LOL)
There is a TON of stuff to see in Philly and I'm sure Boston as well. The amout of time your brother has aloted is really not conducive to seeing three cities. If it were me I'd cut out DC and do that at a later time and include Williamsburg, Yorktown and Jamestown.
Philly and Boston are great for Revolutionary War stuff and the outskirts of Philly and Northern VA are also great for Civil War info.
Living in the Philly area and haveing been to Boston too many times to count I think Philly has a bit more to see and more activites. But I agree, I'd start in Boston do he whole Paul Revere, North Church thing, Check out Quincy Market, Lexington and Concord are great and will be beautiful then. Salem is interesting as well but the history is a bit older.
So as for Philly. The absolute first thing they must do is go to the Independnce Visitors Center. I have to say the Park Service and the City really got this one right. The Independence Visitors center has EVERYTHING you need to plan great tours in one place. You can get tickets there for everything you want to see. The Center also has its own free exhibits and re-enactors that tell stories teach lessons etc. They really need to go there before anywhere else. The US Constitution Center is also a MUST!! It is awesome and the show they have is fascinating.
Other than those they should see Independence Hall and the Liberty Bell of course. The guides and Park Rangers are just amazing. The Ben Franklin house is also neat. the house iteslf is actually gone but there is a map of the city as Franklin knew it at its location. The acutal museum is underground and has some neat stuff.
They can also go to the Franklin Post office on Market Street. This was the very first post office in the US and is still functioning today. They can mail post cards to themselves and get the cancellation stamp that is very "colonial looking" Very often folks from this area will bring their invitation to big events like Weddings, Bar Mitzvahs etc to that post office to get the Franklin Cancellation stamp. Its pretty cool. The Betsy Ross house is neat as is the house where Jefferson Wrote the declaration of Independance ( totally free) the house is not that impressive and they added a huge concrete ugly addition during the bicentenial but to stand in the room where the declaration was penned WOW it give me the chills the same with Congress hall in Independence Hall.
Most of what they will want to see is between front street and say 7th. I have not done it but a carriage ride through " old city is kind of neat" the houses along Pine Street and the adjoining streets were there before the revolution and are still occupied today. Alfreths Alley could be Elfreths not sure is thought to be the first street in the city and is really neat very colonial.
If they can get out of the City Valley Forge Park is beautiful and packed with history but that may be a bit much. If they are here for three days do two days in the city and one in VF. If they have a FULL day in the city then going to Valley Forge on the second is well worth it even if they only have two days. VF is about and hour drive from Center City. There are just too many museums to even name. Ya don't want the kids to get over load though so your brother should be careful.
Food: The City Tavern is where the delegates to the Continental Congress and Constitutional conventions ate. Its still open but under new ownership
Waiters are all in colonial garb and food is sort of from that era, But there are so many great fun places to eat in Philly, Chinatown is awesome as are many of the Italian Restaurants in South Phillly Dante & Luigis, ( they may still have bullet holes in the wall from the mob hits, I like Villa D'Roma ( took the folks from the flybq there a few years ago) and Mara's. Not fancy places at all but great red gravey restaurants. Cheesesteaks of course.
Travel, A car is good if they want to get to Valley Forge. If not I'd say SWA from Manchester NH or KPVD is a good way to go. Train is ok but just as expensive.