Foliage color will still be good in many areas of New England but you should be able to get reservations for Sun thru Wed. Some seafood restaurants on the Maine coast will not be open during the week that late in the season but you will still have a lot of choices.
I think I would choose the Rockland ME area. In case of bad weather you have the Farnsworth Art Museum, Freeport shopping to the south and also the option of visiting Portland coming or going.

Wolfeboro Inn, Bayside Inn in Alton Bay, The Balsams in NH?

Think about taking the Amtrak train from Boston to Mystic CT.
http://www.mysticseaport.org/
There is always something interesting going on at the Mystic Seaport. You would not even need a rental car there that would have to be returned to Boston. Unless you already have the return tickets bought (from Boston) you could fly home from NYC or even Newark NJ.

Thanks for all the suggestions. Would also like to consider something in the mountains where we might have to curl up inside due to the weather. I know that must be heresy for those of you that live in New England!!! After all the heat, burning sun & drought of Texas, something lush, cloudy/rainy would be such a welcome for us.

You'll be right in the middle of foliage season, perhaps slightly past in a few northern mountain areas.

Mountainous areas (or at least very hilly) are found in several areas of New England, including The Berkshires, Pioneer Valley (Amherst, Northampton, Deerfield, etc.), Vermont's Green Mountains, New Hampshire's White Mountains, and the Acadia National Park area in Maine. Chances of encountering chilly and perhaps rainy weather could happen in any of these places.

Thanks Bachslunch. Does anyone have any suggestions for lodges in any of these areas?

Several years ago we stayed at the Golden Eagle resort in Stowe VT. The units in the back had large rooms, balconies, gas fireplace, and a nice little reading nook. We opted for a jacuzzi but the other choice is a mini kitchen. That far north, the color will probably be past peak by your dates.

Based on location, I might choose this place
http://millfalls.com/inns/the_cottages.htm
Haven't stayed there, this is close to where we live. The lake is beautiful. Meredith gets a lot of traffic but is a very pretty town. The mountains are just a short drive north. Center Sandwich is one of our favorite areas (near Squam Lakes). You can drive east from Meredith to Center Sandwich and then thru Tamworth to connect with Rt 16 where you can head north to North Conway (huge tourist area) or loop back via the Kancamagus Hwy. Tourist hiking includes The Flume but there are hundreds of hikes in the area. Again, for your dates, this may be slightly past peak but still beautiful.

You might look for suggestions in the Monadnock area of NH. Pretty rural. Several old inns. Some hiking opportunities.