I'd recommend taking the route through Canada. Take I-94 to Michigan, and cross at either Detroit or Port Huron (I-69), and drive through Ontario. You can cross back into the US right at Niagara Falls and take I-90 the rest of the way to Boston.

Or if you don't want to visit Canada, you can just take I-90 the entire trip, going south of the Great Lakes through Cleveland.

The total travel time shouldn't be that much different between the two options.