I don't know where you are coming from or how you are traveling, but here are some places that are fun to visit. You will need to decide soon, though, because early to mid
Vermont is leaf peeping season, and northern New England is packed.

From the south:
Mystic, CT: an aquarium, the Seaport outdoor museum of old boats and ships, fun places to eat.
Newport, RI: summer "cottage" mansions, scenic cliff walk along the ocean, lots of fun bars and restaurants, across the river from scenic Tiverton.
Nantucket, MA: lovely houses, quaint cobblestone streets, romantic walks along the beach or on the moors, sailboat ride before mid October
Boston: everything. Just don't go there the third weekend unless you like crowds. It is Head of the Charles regatta, great fun but thousands of rowers crowding hotels and restaurants.
Portsmouth NH: great walking town, brew pub scene, Wentworth-by-the Sea, a beautiful Marriott resort in historic building just outside town
Portland, ME: foodie scene, good walking town, ferries serve local islands and make a nice ride, easy daytrips to LL Bean in Freeport, Brunswick and South Harpswell and other islands
Burlington, VT: pedestrian downtown with great scene, Hilton has views across Lake Champlain, Shelburne Museum, outside town is an outdoor museum of NE life.

All these places are linked by generally great scenery (White Mountains, Green Mountains) and classic villages.

One sort of TMI advice: there is a temptation to go to a "romantic country inn". In many of them, you can hear every sound in the next room. Not my idea of a honeymoon.

Definitely Newport, RI. In itself, it's not a cute port town (too big for that), but there are some really nice hotel properties there, such as Hotel Viking (I've stayed there a number of times), Castle Hill Inn, the Chanler at Cliff Walk. IME, this site looks like it has a very comprehensive listing of all Newport hotels. (Not a booking site; links out to the individual hotel websites.)
http://www.destinationnewport.com/hotel.asp

October is too cold to hang out on the beach, but Newport has a number of them that are nice to walk on at least. There is lots to do in town itself, and Boston is less than an hour and a half away for your day trips. Additionally, RI has an extensive network of public bike paths, one of which stretches from Newport along the coast to East Providence.

From there to see cute port towns, you could drive south to the CT border: Mystic and the small quaint towns nearby like Old Stonington.

Oh, and anywhere in New England, especially the southern part, will have plenty of American history for your fiance! From Newport, Lexington and Concord are less than a 2 hour drive; Salem is farther away but still accessible as a day trip.

Not sure about resort-like places near the coast. You are too late for swimming/sunbathing - and in the northern areas some places will be closed for the season. Further south and in leaf peeping areas things will be open much longer but also very crowded.

I would allow at least 3 days for Boston - assuming you do Lexington and Concord from there. And then head either inland for leaves or along the coast for fall beaches and cute towns.

It would help to know how much time you have, how you will be traveling (assume car - pubic transit would be very challenging) and how you will be getting there (flying in and out of Boston or ?)

I agree with nytraveler that we need to know how much time you have. Boston is a great city (the largest in New England), so it is a must-see, especially for history buffs. From Boston, you can take a day trip to Concord & Lexington & walk along the Minuteman Trail (of Paul Revere fame); have lunch at the Concord Inn; visit Louisa May Alcott's home.
You could also spend a day at Old Sturbidge Village.

Portland, Maine, is a lovely city, too, similar to Boston but smaller. Perhaps you could stay one night at Wentworth by the Sea in NH, on your way to Portland. Stop at seaside Maine towns to see the ocean, such as York, Oqunquit, & Kennebunkport.

If you have the time, & depending when in October you are coming, you could drive to Bar Harbor Maine & Acadia National Park, which is beautiful. There are some easy hikes. But not sure when everything closes.

I like the idea of Newport, RI, too with its mansions, beaches & cliff walk. We had a drink last year at Chanler on the Cliff Walk, & it is a gorgeous small hotel with beautiful ocean views. We also like Hotel Viking, as ggreen suggests.

Another idea is to head inland from Boston to the Berkshires -about a 2 - 3 hour drive. The mountains are not as high as Green Mountains or White Mountains, but they are still very pretty, with hiking trails, & some great museums, such as Norman Rockwell, Clark Art Institute & MassMoCA.

It is a bit pricey but the Ocean House Hotel in Watch Hill RI would give you what you are looking for before Boston. It is a re-do of one of the old sea side hotels from an era past, with the modern amenities. It even has a croquet court as well as . I've only been there for lunch on one of the beautiful porches, but the site is fantastic, a real classic. You would be very close to Mystic, Ct, and not too far from Newport.

If you are on the Cape take a look at Chatham Bars Inn and also at the Wequassett Inn. Both resorts are wonderful honeymoon destinations, you won't hear the other honeymooners enjoying their visit, and the rates are bit lower than they are at the height of the summer season.

And the Cape Cod Rail Trail will provide excellent opportunities for biking.

<<<visit Louisa May Alcott's home>>>

and Ralph Waldo Emerson's, and Henry David Thoreau's (including Walden Pond)....

Are you flying to New England, or are you starting out there? If you do fly, and take some of the above suggestions, consider flying into Providence instead of Boston -- it's a really easy airport to navigate, and very close to some of the named towns -- Newport, Mystic, Stonington, Watch Hill, for example. If you're going to head north of Boston, then flying into Boston makes sense, of course.

New England is beautiful in the fall and lots of cool places outside of Boston! There are some really lovely little "authentic" New England towns throughout Massachusetts as well as great hiking trails. Driving through the Berkshires, the Mohawk Trail (route 2), check out the Glacier Potholes in Shelbourne Falls. The M&M trail becomes part of the Appalachian Trail and have wonderful hiking opportunities. If it was me, I'd stay somewhere in western Mass (much cheaper than Boston area) and visit Boston for a few days to see the sights. New England is very drivable and you can get to Vermont and NH within a few hours from Mass. I'd be happy to offer more personal advice if you have specific questions.

The important thing is to get on hotel reservations soon. The leaf peepers are out in full force in late September into October and hotels fill up fast in N.England.

newport and nantucket are excellent suggestions... both have lots of B&B with charm and in oct., mid-week might offer some deals...

portsmouth, nh is another great place, smaller and less travelled--1 hour+ north from boston...look at sise inn or in newmarket, NH the fab old marriott wentworth by the sea, an historic hotel..