An evening walk along the MIT waterfront will reveal a wealth of great locations for images of the Boston skyline. You will find a marina, the Harvard bridge, several crew houses, the Longfellow bridge, and stunning views of old Boston. If you are visiting, make sure to bring a variety of lenses. The Charles is quite wide and you will need a longer telephoto to get closer to the distant shore.
Feel free to use my Boston photo map as forward recon.
Camera: Nikon D300
Lens: Tokina 11-16