Of note: the Blue Water Bridge (on I-69/I-94 crossing into Ontario) is a toll bridge.
Your route across southern Ontario, using the Alexander Pkwy and Red Hill Valley Pkwy through Hamilton (both freeways connecting ON 403 to the QEW) should be fine…I did a very similar route in early April and easily made it across in about 3 hours. I'd suggest getting gas while still in Michigan, though.
Since you're going near Niagara Falls, might as well pop down. It's $15 to park on the Canada side, but it's a much better view than the New York side.
Unless you have a dire or compelling reason to swing south through Binghamton, NY and along NY 17 and I-88 OTHER than toll diversion, there are plenty of routes that parallel the NYS Thruway that don't involve tolls or such a lengthy diversion. In particular, you could take the completed segments of the Lake Ontario State Pkwy between Niagara Falls and Rochester, I-490 through Rochester, I-690 through Syracuse, NY 365 to NY 49 via Rome and to Utica, or NY 5S between Utica and Herkimer.
If you don't mind swinging north for a bit through Vermont, there's a toll road to the top of Mt. Equinox near Manchester. And *VERY GOOD* gouda cheese at Taylor Farm right on VT 11 just west of Londonderry.
As you're going through Concord, NH, you could stop at the NH state capitol building.
For Rhode Island, I'd detour through Newport (MA 24 to RI 24 to RI 138). VERY neat coastal town with lots of history. Be sure to drive Ocean Ave and grab a lobster roll from Flo's Clam Shack.
The Baltimore Inner Harbor is pretty neat.
Within the Northern Virginia sprawl near Dulles Airport is the Manassas battlefield (Civil War).
Two of my favorite scenery drives in Northern Virginia are along SR 601 from the US 15/VA 234 intersection (north of Haymarket) to The Plains, and along SR 734 in Loudoun County, from US 50 Aldie to VA 7 Bluemont. The former is not too far off I-66, while the latter is a leisurely slant up to the VA 7 corridor, which is a 4-lane corridor from Leesburg over to Winchester.
If you have time and don't mind a slight detour, an even better scenic drive is along SR 635 across western Fauquier County. Take I-66 to Exit 27 Marshall and turn left, then take SR 647 down to SR 635. SR 635 ends at US 522, which you can then take north through Front Royal and back to I-66, or you could continue north on US 522 to Winchester.
From Winchester, an alternative to I-81/I-70 is to take US 522 to Hancock, MD. It's more direct and is a 4-lane road in Virginia with the only real slowdown being Berkeley Springs, WV.
West of Hancock, you can stop at Sideling Hill on I-68 in the middle of a VERY impressive rock cut.