How are they empty? People are in them every week. St. John's the Divine isn't even completed yet. NYC just has different politics, which says nothing of its religious tradition.
New York City is laced with churches. That is a fact, but that fact can not be used to signify that that City has a meaningful spiritual life. Certainly there are faithful people who attend them, but those faithful people are in no way influential in the city's political life, which like San Francisco's has caved to the basest human instincts. The Red States elected Bush largely because they thought of him as a moral leader. I dare say no one could ever get elected in New York City on that basis.