So, what are you interested in? New England may be reasonably small, but there is a lot to do here.

If you are looking for foliage, it can be vary from year to year and week to week. There are a couple of networks that try to identify where is "peak" including the foliage network, Jeff Foliage, and Yankee Magazine. Generally speaking, peak north of the whites is last week of September, my favorite time in the white mtns in NH or Green Mtns in VT is last week of Sept and first weekend of Oct, and then after that, it tends to be better south of the mtns. We've had pretty good years the last 2-3 years, but prior to that was a run of about 6-8 bad years. If heading to the White Mtns with kids, there is Storyland and Santa's village. Also, with kids, if interested in hikes the Lost River Gorge or the Flume in the white mtns are probably the easiest access. If you want views, near Burlington VT a gondola goes to the top of Mt Mansfield and the same in the White Mtns for Cannon Mtn (ski resort lifts that are in operation).

If interested in lighthouses, Nubble and Portland Head are short drives.

Depending on when you are here, fall festivals, corn mazes, pumpkin patches, apple picking are all the rage. Usually starting end of September.

Fall is off peak for cape cod, so a great time to head down and also a time when you can drive your car on a lot of beaches (check local rules)....so a lot of people drive onto beaches and have fires.

The witch museums of Salem, MA will be getting going in October and can be fun (granted, I haven't done them in 20 years).

Boston has a pretty good aquarium (its ok, but kid friendly and easy access), the Science Museum is great (again, thinking of kids or big kids like me), and they have good harbor cruises. Jerry already turned you onto the North End. Great Italian. My favorite is actually the pastries. Mikes is the famous one, but Modern may be better. All of that is on Hanover St. in the north end....short walk from the aquarium. As for restuarants in Boston, I'm a fan of Stephanies (a local chain...usually Stephanies on Tremont or Stephanie's on ....). One of my favorite Mexican places is Temazcal over by the seaport. Series of good restaurants over there with a boardwalk with good views of Boston and/or the harbor.

If I were to do an itinerary, depending on how much time you have:

2 days in Boston: Aquarium, Museum of Science, Old Ironside, Faneuil Hall, etc.
Drive up to Conway, North Conway, Lincoln, or Jackson NH, 2 days: Storyland, over to Santa's Village, Flume Gorge or Lost River. Maybe also a train ride out of North Conway. Drive the Kancamagus Hwy and loop through Crawford Notch. If have time, either drive to the top of Mt Washington or take the Cog Railway.
Over to Burlington VT for 1-2 days, tour Ben & Jerry's factory, go to the top of Mt Mansfield, hang out at Church St in down town Burlington, maybe take a harbor cruise on Lake Champlain.

Any of those could be expanded or shrunk. And you can add in a number of other things as you'd like.