There are a multitudes of Japanese gardens in Tokyo that you can stroll and enjoy.
The new "Sky-tree" is a very impressive structure, much much bigger than the Eiffel-copy they have in the center of Tokyo.

Google a bit to find the locations (like "temples tokyo", "gardens tokyo" etc).
You can get a pretty good skyline view of tokyo from Odaiba ( http://en.wikipedia.org/wiki/Odaiba ), which has a ferris wheel and a few strange buildings and stuff.
If you are there on a Sunday, go up to yoyogi-park to watch Elvis-people and young girls dressing up in cosplay-costumes.

IMO, the people and styles of Tokyo is one of the coolest things to photograph there ^^