There are several places to go in New England in the fall and a few have been mentioned.
Ditto on Mystic Seaport area, it's wonderful. Lots of historical stuff there, great dinning opportunities as well.
Acadia, another excellent location. Rocky coast and everything Glenn mentioned.
Green Mts are also quite nice, smaller than the White Mts in NH but still quite pleasant in the fall. There are a lot of fall festivals in Vermont as well. In a way the Vermont area aims towards the NY tourists.
Western Mass in the Berkshire Mts, have several back roads, Boston Pops Summers in that local. Red Lion Inn in Stockbridge, Ma. wonderful old hotel, nice size rooms, all decorated in antiques. Norman Rockwell museum is right down the road. Main St. is kept in the same design as Rockwell's famous painting of Stockbridge. The area also has many lakes and streams for fishing, canoeing, etc. It also has the original Yankee Candle factory which is an interesting place to tour, as well as maple sugar farms but fall is the wrong time of the year for sugaring.
White Mts, Conway NH area is another great place to visit. Mt. Washington is there, quite a trip but you can take a train up the mountain and save your vehicle it's struggle to get up to the top. Antique shops abound as well as state and National Parks and as someone mentioned there's a couple covered bridges in the area.
There's always Cape Cod and the Islands. They all have great B&B's as well as a quieter lifestyle in the fall once the tourist go home. The colors of fall are there but not as accented as the mountains. In my experience, NH had the best fall foliage but that could have been the seasons I went there and not in some of the other locations.
Hope that helps. You might spend some time at Yankee Magazine's website. They highlight different areas and have excellent pictures and articles about life in New England. They even have a section on fall foliage.
http://www.yankeemagazine.com/
Lynn