Taking the metro in Tokyo is an experience in itself if you are coming from Europe.
The metro is a lot more packed but also a lot more civilised. At any given time of the day, it will be busy! Peak Hours for businessmen is usually around 21h30 once they left the office and finished their drinking session with colleagues for example.
Mornings are a challenge where you are literally squeezed in coaches by the flow of people and little chance to escape, when the coach opens at the platform, you are also literally expulsed by the pressure released!
Shinagawa at 15h00, nothing crazy, midday!!