A great spot a good friend told me about, for shooting the night skyline with the Longfellow bridge in the foreground and the John Hancock and Prudential Center in the background, is the top of the parking lot at the Museum of Science.
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This was taken right after sundown using a tripod and a long exposure which makes a train passing on the Longfellow appear as a long yellow streak. Different timing on your exposures, if only by a few seconds, can change your light from blue to purple to black as night.
Be sure to use a shutter remote because even the slightest movement of your finger pressing the shutter can cause the image to become blurry. If you don't have one you can always use the camera's self timer.
If you're luck enough to get a semi-cloudy sunset, you're in for a nice surprise as the shapes and positioning of the clouds add so much more to the character of a photograph.
Now time to move across the parking lot over to the other side before losing all the light and take in the sight of the Zakim Bridge all lit up. Certain times of the year the Zakim is lit different colors but I have yet to get there when it's anything other than white.
If you can get your hands on a wide angle lens, USE IT! It's so much fun to see all you can capture in the frame and it can make the most unusual images.
There are numerous resources on the web with tips for shooting at night. Here are just a few.