Lol, since evidently no one's real familiar with Boston, I'll mention a couple trips I took out this past week.
One great trip starts at the "Paddling in Boston" Kayak launch site on the Charles River on Soldier's Field Rd, out by Newton/Allston (Exit 20 off the Pike). If you take the Charles west towards downtown Boston, you get some really incredible views of Commonwealth Ave area (Prudential Building, Hancock Tower, etc), as well as obviously all of downtown. Coincidentally, this is where the fireworks happen on July 4th too. MIT is on the Cambridge side of the river, and it really is a beautiful stretch. Once you get out past the Harvard bridge, you start running into some minor chop. At the mouth of the Charles, if you turn right, you run right into the Harbor. Paddling out, following the contour of the land brings you to South Boston (the best part of the city, no doubt!), and around Castle Island. After Castle Island, across the channel lies Thompson and Spectacle Island. You can camp on these islands, and Spectacle Island offers a great view of the whole harbor and Boston.
It takes about an hour and a half - two hours to get from the launch site to the mouth of the Charles, and from there it's about another 2 hours to get to Thompson Island.
Anyway, hope this helps someone!