Wow, no answers yet?

There is no difficulty finding a spot which overlooks Tokyo, the highest point with such a view would be Mt Fuji itself. Unfortunately, the days when the air is actually clear enough to enjoy a view of the city are few. Pollution isn't necessarily bad here, but the city lies near the sea, so the air is often hazy.

Takao-zan (Mt Takao) is easily accessible by train from Tokyo, and is a relatively short distance away. It is not a difficult climb, and offers wonderful views. But once again, how much you will see will depend on how clear the air is.

Your best bet for overhead city views would be from the tops of the many tall buildings in Tokyo, or Tokyo tower. The best of these tall buildings would be The Mori building in Roppongi hills. It is one of the few buildings with an observation deck on the roof, and the views in any direction are breathtaking, day or night. If you feel the need to hike, you could always take the stairs.

Try going to the Tokyo tower at night. The night scenery is great to look at.

Tokyo Metropolitan Government Building - Wikipedia, the free encyclopedia

I have been here a couple times. Great view. I believe it is one of the highest points the public can go to (for a fee).

I can see that building from my GF's apartment right now.

It's one of my favorites...though from the top floor you can feel a bit of a sway, which made me uneasy.