Baltimore, "The City that Reads" under the previous administration of Kurt Schmoke, ranked 25th, albeit it is claimed to have 40% functional illiteracy rate. I think what put as ahead of places like NYC or Philly is a relatively low population and the concentration of cultural institutions serving mainly suburbs.
This points to a certain distortion by the study, which seemingly does not take into account the effect of the economies of scale and the niche character of the cultural commodities market. New York may have a low per capita scores due to the enormous size of its population, but the sheer size of the city can support a large number of cultural/literary institutions, which makes it the cultural capital of the United States. These institutions, moreover, serve a market niche composed of a fragment of the total NYC population - whereas most New Yorkers live blissfully oblivious of them, if not functionally illiterate, and meet their cultural needs mainly by watching television.
Wojtek