http://www.fodors.com/community/united-states/new-england-road-trip-415442-2.cfm

I hope this thread will help you

Do spend a few days in Boston, there is a nice children's museum and an aquarium there. Most towns have elementary schools with playgrounds that are open to the public after school is out.

There are a couple of different agricultural fairs on weekends during that time period. If you go first thing in the morning you can usually have a nice breakfast at a community/church booth, watch the 4-H kids get their animals ready for the day, visit the animal exhibits and avoid the crowds that will come in later when the midway opens.

Our youngest gd's kindergarten class visited the childrens museum in Dover NH last spring and she liked it very much. It used to be in Portsmouth near Strawbery Banke. This would be fairly convenient to southern Maine should you stay in that area. Portsmouth is a great downtown for walking, looking at boats, etc. Last year we visited the farmers market in Portsmouth which was located next to a very popular children's playground.

York ME used to be our family's favorite beach town when we were younger and one of the relatives had a cottage. Great beach. Nice walk to Nubble Light. Fun watching the taffy pulling machine at the Goldenrod. Not sure about York's Wild Animal Kingdon/amusement park. A couple of years ago we spent a weekend at the Dunes in Ogunquit ME which is a perfect family location. They have units ranging from motel to full cottages. Although located on Rt 1, they are set way back from the road with a lovely lawn area and winding paths. We just had a one bedroom unit and even that size had a table and adirondack chairs in their own little area. Great place for afternoon relaxation and plenty of place for a toddler to play. Southern Maine is not my favorite area but off season, I didn't mind and really liked the Dunes. With a toddler, you want a big enough place to stay so your son can nap while you do something else.

Apple picking is in full swing. Several orchards offer hay rides etc. If you are in the Concord NH area, Beech Hill Farm has animals to visit and a giant sand pile with toy trucks for visiting kids.
http://beechhillfarm.com/
There are several very nice school playgrounds in the area.

Storyland in Glen NH is in the mountains and very popular. Good for the pre-school set but 2 might be a little too young.

Is there good flight service from your city into Manchester NH, Portland Maine or Providence Rhode Island? Boston Logan Airport car rental rates are sometimes twice that of the other cities due to high fees and taxes, so if youre renting a car for two weeks it might be worth exploring your other arrival options.

Agree with Clarkgriswold...if there is service from your home city to one of the smaller airport you might save some big$.

Also, while overall Septemeber is a beautiful month in New England, plan on the "Beach" portion early in your trip.

You might think about starting out in Newport RI area for a few nights. Lots to see and do there, also has beaches. Then up to the Cape for a few nights. The you have a decision to make, do you want to spend some time in the NH/VT mountains or do you want to do the Maine coastline? Pick one, then after that finish off in Boston. 2-3 nights in each place gets you right in your 10-14 day period.