Tokyo is such a huge metropolitan.
How about seeing Tokyo from Observatories of the Tokyo Metropolitan Government Building in Shinjuku?
They have two observatories(North/South) in the main building.
Admission: Free of charge. No reservation necessary!!
Service hours: 9:30 a.m. – 11 p.m.
*During the year change period, it will be closed. >>More info
On a clear day, you would see Mt.Fuji from observatories!
I recommend to visit there at night for great night view, as well.
the Tokyo Metropolitan Government
10 min. walk from “Shinjuku” station