CORRECTION: Oops! It turns out the Staten Island Ferry does let cyclists on board from a ground-level outside entrance reserved for cyclists. Egg on my face, but I'm glad to know that I was mistaken.
I had a breathtaking sunset ride yesterday down the Greenway from Inwood to Battery Park. Upon reaching the Battery, my friend and I entered the Staten Island Ferry station to freshen up and hop on the 1. Imagine my surprise upon being apprehended by security and being told that we could not bring our bikes upstairs (where the restrooms are) because they might be injurious to other patrons (who might, for example, snag their clothing on them). I was flabbergasted--do they make the same statement to individuals with strollers or in wheelchairs? Does the Staten Island Ferry truly not allow bicycle commuters (despite allowing bicycles on the ferry for the 5 Boro Bike Tour)? What kind of green transportation policy is this? Bicycle commuting is not a real option for most New Yorkers unless (a) bicycles can be stored in a safe place when not being ridden (for example, the office) and (b) cycling can be combined with other modes of mass transit (such as trains, subways, and buses).
Conclusion: Fold up the bicycle and stash it in the camo bag before entering unknown buildings. It's a jungle out there.
Have you had similar bicycle-hostile experiences in New York? Report them here.