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In mid-September, the foliage isn't near its peak in most areas of New England, so you'll most likely catch the colors just starting to change. Of course, that doesn't mean you shouldn't spend some time in the area. It seems you have one week solidly planned already, so you still have another week to explore various areas of New England - you could head from Cooperstown up into Vermont for a couple of days, into New Hampshire for two more, and then start heading towards NYC for the remainder. If you wanted to, I'd say you have time in here for a visit to Boston.