The train system in Tokyo is incredibly well developed and runs efficiently. It can get slightly confusing, however, as it is not one system. There is the Metro, the JR line, the Ginza line, and a few others, all of which require separate tickets (which can be purchased as combo tickets). Takes a day or two to understand how it works. Also - Tokyo is MASSIVE, so it is a major key to plan accordingly so you don't wind up going from the equivalent of the UWS to Cobble Hill over and over.