Not sure how you are planning to get around without renting a car - I mean, you have to somehow get between Boston, Philly and Niagra Falls and obviously they are hundreds of miles apart.
I would make sure you start calling some hotels and get some reservations in place, because sometimes we've tried to get something last minute and come to find out there is a convention in town, everything is booked, etc.
Can't comment much on Philadelphia, since I've never been there, but I would agree, the Canada side of Niagra Falls is fine, the American side is a bit more shady. Did live in Boston for a year and would agree, it's about an hour's drive to get to Plymouth and the historical sites there. As for Boston itself, you can check out the Freedom Trail, Fanuiel Hall, Old North Church. If you stay in downtown, most of the popular spots may be within walking distance depending on where you stay, but the "T" (Boston's subway system) makes it pretty easy to get around. If the Red Sox are in town, and you are interested, you could try getting tickets to a game, but most likely, they are all sold out, and you will have to pay a small fortune for decent seats through a ticket broker.