I cannot stress this enough! There will be tour buses (literally) full of people. All of the above recommendations for sticking to small towns in southern NH or central Mass. are excellent.

The color here in central Mass is beautiful right now, and should remain so for about two weeks. Don't worry about "peak." Some of the brightest colors are those that appear quite early in the season, while there's still alot of green around. Tower Hill Botanic Garden in Boylston (http://www.towerhillbg.org) is a beautiful spot with great views less than an hour from Boston, and while a drive north from there on route 140 won't take you through the absolute quaintest New England villages, it will have little traffic and some lovely scenery. It goes past Mt. Wachusett ski area, whose chair lift will be running for the benefit of leaf-peepers.

Whatever you choose, you will enjoy it.