Does it cover subways?

Hi Gully,

Yes, the JR Pass covers all JR trains: Local, Express and Shinkansen (except the Nozomi and Mizuho classes), so will cover all the JR lines in the JR East region map you show.

Please note that the map is showing mainly above ground trains rather than subway. As you can see you can get around very well in Tokyo using JR services, however as the Tokyo subway is not operated by JR you will be unable to use the Rail Pass on it. In Kyoto you will need to purchase individual subway tickets or day cards as the internal JR system is not as extensive as that of Tokyo, however if you get to Osaka you will find a good coverage of JR lines free for use with a Japan Rail Pass.

Hope this helps!