NYPIRG's Straphangers Campaign has rated the cleanliness of subway cars for the period of September 14, 2010, through November 20, 2010, and compared the results to approximately the same period in 2009. They examined the floors and seats of 2,000 cars to see how well they were being cleaned. Litter didn't get counted in compiling the ratings.
The MTA's survey showed that 94% of the cars were clean in 2010, but the Straphangers Campaign's survey came up with 47%. The Campaign explains that
The Campaign acknowledged the different findings, but said that it was not able to point to factors that come to these results.
The car cleanliness surveys by Transit and the Straphangers Campaign’s surveys use similar although not-identical methodology. For example, we rate throughout the day and night and on weekends. New York City Transit rates on weekdays between 8 a.m. and 10 p.m.