About my Tokyo travel:

• I want to know the best places to visit in Tokyo!
• I want to see Mt Fuji

Welcome to Tokyo! To see Mt Fuji, Tokyo Tower or Sky Tree is the best spot:)

How if I plan to go to Mt Fuji itself? and on the way back stop at Gotemba FO?

You mean, climbing Mt Fuji? If so, you need to stay at a lodge near the top, and it's a very tough hike.