Very close to Tokyo Tower and Zojoji Temple, there is the World Trade Center Building which is rated to be in the Top 10 best views of Tokyo by TripAdvisor. On clear days, not only can you see Tokyo Tower and SkyTree, but you can also Mt Fuji in the distance.
The observatory is open from 10am to 8:30pm with entrance ending at 8. Honestly, one of the best you can get for the super cheap price of about 500 yen.
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