Didn’t read the whole thread, but there is a company that does Segway tours. 
http://www.bostongondolas.com/
The gondola ride at sunset is hopelessly romantic!
You are wise in not renting a car. Driving is confusing and scary, and parking is scary and expensive. The T will get you close to most anywhere, and Boston is small enough to be a comfortable walking city.
In addition to the above recommendations, I will suggest the Isabella Stewart Gardner Museum for an amazing afternoon. http://www.gardnermuseum.org/
If you’re in the Quincy Market/Faneuil Hall area (which you undoubtedly will be at some point), be sure to walk up and see the Holocaust Memorial. http://www.nehm.com/location/. It’s right across from the Union Oyster House and (I think) on the Freedom Trail. It’s striking in its design and unforgettable in its presentation. Enter from the end farthest away from Faneuil Hall for the best experience.
For a cheap, sports bar meal, try the Pour House on Boylston, across from the Pru. Lots of brews on tap, large menu, and really the cheapest dinner I’ve ever had in Boston. http://www.pourhouseboston.com/ They even do breakfast.
I second the Top of the Hub. Dinner is expensive but you can go up there for just drinks as well. Especially recommended if there is a full moon.
Nice weather + seaside = **The Barking Crab **for a lunch spot. Not the greatest food, but cheapish and right on the water.
And they haven’t been busted for health code violations in over two years!
Thought I’d report back, as we went on the trip this past weekend.
Beautiful weather! Hit many of the spots and stops recommended…
some highlights:
Union Oyster House… really enjoyed it! Chowdah was good, but probably the best part of the experience was the special draft beer Sam Adams makes just for them. GOOD stuff. We waited an hour or so for the table, but we didn’t mind, just chilled at the bar in the meantime. The Mrs. had oysters that she said were pretty good.
Freedom Trail walking tour… a great way to see the sites w/ a guide and get the stories behind some of the locations. To think the “New” State House is from the 1790s!
Bunker Hill Monument — we made the climb up the 294 steps to the top. Ugh! Amazing views as a reward though.
Duck Tours — I DID get to steer the boat on the Charles River woohoo
Went by the Barking Crab, it was near where we stayed… too busy to stop by. We went to a place called No Name Restaurant instead. Not bad.
Made it around Faneuil Hall and Quincy Market a bit. We wanted to get up to see the armaments museum on the top floor of Fanueil, but I guess they’re closed on weekends. We toured the Old State House, walked the North End, the Old North Church, and across the bridge to the USS Cosntitution.
Oh and FENWAY! Got a guided tour of Fenway Park, stood on the Green Monstah and in the press box.