In Boston proper, do the freedom trail. There will be a lot of "Tourist Traps" but the walk through Charlestown and North End will be amazing. When I bring folks in from out of town, they say that these two places feel like they're out of a movie.

For a winter day-trip from Boston, I would suggest  Rockport (Massachusetts),  Newburyport or  Portsmouth (New Hampshire). All awesome New England Towns that have many of the things you're looking for.

You're definitely going to be in the right area for wine and beer on the east coast. Upstate NY's Finger Lakes region is a criminally underrated wine culture - my favorite, when I was living there, was  Anyela's Vineyardin  Skaneateles. Partly because of the town. I've heard that it's become a little touristy these days but I can't imagine that spoiling the experience - it's an absolutely beautiful area. As for beer, Syracuse has a small but passionate craft brew scene. While I was living there I was quite fond of  Middle Ages Brewing Company (though I'm not sure if they're giving tastings or tours these days.) For a great sampling of the beer culture be sure to visit Blue Tusk in the Armory Square, in the heart of downtown Syracuse. It's a great little area that has really started to blossom - in my absence, of course, haha. I know that you mentioned Buffalo and Syracuse, but I would absolutely not miss a chance of going to Rochester (New York). I cannot recommend just wandering around there enough. Staying with the beer theme, a good base of operations there would be Tap and Mallet. That entire neighborhood just has very good vibes and friendly people. I hope this helps, enjoy your trip!

If you'd like to take a day trip outside of Boston, I highly recommend Salem (Massachusetts). First of all, the drive is beautiful. It's a town of cobblestone streets, rich in semi-spooky history, and actually has some pretty great East Coast pizzerias. I would recommend avoiding any of the actual tours/guides that inform about the Salem Witch Trials. Instead, read up on the history in advance, locate the historical places you're interested in seeing, and self-guide your own tour! It is not to be missed! I went four years ago and it was still one of my favorite memories of Massachusetts!

Cambridge is right across the water from Boston, but can feel like a whole other town. I really like The Charles Hotel, located right in Harvard Square. In fact, the entirety of the square has some great gems like the awesome hot chocolate at L.A. Burdick Chocolate, kitchy gifts and historical artifacts at Leavitt & Peirce, and you won't miss the long line for hamburgers right across from the Harvard campus at Mr. Bartley's Burger Cottage.

A few minutes drive deeper into Cambridge, you'll find the MIT Campus where there's the awesome MIT Museum (Building N52) -- lots of robotics there, if you're into that, like I am -- and the Miracle of Science Bar & Grill. The food itself is nothing to write home about, but the menu is fashioned after the periodic table and the conversation over-hearing is second to none. Enjoy!

The seaport area of Boston has just recently been developed into an area with lots to do (and eat!).  There are lots of great restaurants there, including Legal Sea Foods.

Letchworth State Park is called the "Grand Canyon of the East" and is well worth a visit, although I'm not sure about Christmastime. 

I would definitely take a drive up to Niagara Falls.  Better to cross the border since the view is better from the Canadian side.

A fun day is to visit Gore Place in Waltham, MA which is a Federalist mansion built by Gore who was a politician banker & lawyer in the 1800's.  There are excellent restaurants in Waltham on Moody Street.

Italian: Il Capriccio or Cambodian: The Elephant Walk.  Have fun.

Buffalo has tons of breweries.