I just ran into an exceedingly useful web site sponsored by New York City "straphangers" organization. Straphangers is a local term for transit users. The organization is also a project of the New York Public Interest Research Group, an organization usually associated with liberal causes and activism.
The Straphangers Campaign just recently released their annual report card on the city's subway system, comparing performance subway line by subway line. As they describe it:
"What do subway riders want?
"They want short waits, trains that arrive regularly, a chance for a seat, a clean car and understandable announcements that tell them what they need to know. That’s what MTA New York City Transit’s own polling of its riders shows.1
"This "State of the Subways" Report Card tells riders how their lines do on these key aspects of service. We look at six measures of subway performance for the city’s 22 major subway lines, using recent data compiled by MTA New York City Transit.2 Much of the information has not been released publicly before on a line-by-line basis. Most of the measures are for all or the last half of 2008.
It's well worth a read.