We did Thunder Bay to Toronto once and the Trans Canada highway is way too busy .
The Eastern Maritimes is good as is the Rockies. If you want more flat, I'd put my $ on the maritimes. Newfoundland, PEI, New Brunswick.
Good thing too its only a short flight from Europe and easy access from New York airport. Montreal would also be a good starting point.
www.crazyguyonabike.com seems to be the best for cycling info