I loved the Hilton Shinjuku. I loved the Shinjuku area.

Topcare has given a couple great options that are Japanese chain hotels. They all are high rises with great views. The Royal Park I stayed at in Yokohama was a Japanese chain, and my room was on the 63rd floor and was amazing.

There are quite a few western chains in Shinjuku as well. The Hyatt, Hilton, Kimpton, and Park Hyatt are all a couple blocks from each other.

Then there are a bunch of Marriotts and Sheratons over in Shiodome area.

I think you figure out what part of Tokyo you want to stay in, and then most hotels will be high rises in those areas. With city views.