Flying into Boston and out of Washington DC is a good and practical idea.
Keep in mind that Niagara Falls is on the opposite corner of New York State from New York City. It's an 8 hour drive non stop with no traffic from Boston, and a 7 hour drive from the falls to New York City non stop, no traffic.
And there's always traffic.
I'm +1 for taking the train between Boston, NYC and Washington DC. Besides traffic, parking is difficult and expensive.