Though trains (subway and above ground) are very efficient and plentiful, in and around Manhattan, when it comes to their state, cleanness and overall sanitary state (for trains and their stations), there is no comparisson to those in London, Berlin, or Tokyo, to mention a few. NYC trains and stations are in a state of disrepair.
Yet, there is no better way to traverse the city than taking trains. Owning and driving a car in NYC is borderline pyschopathic—which, coincidentially, could also be said about Tokyo.