As much as I would like to lay the blame at the feet of Napolitano, my guess is this is a case of a bad situation that ALL of the service providers at JFK weren't equipped to handle. PA personnel and snow equipment probably weren't able to keep up. Ground crews were more than likely very short staffed. With large portions of NYC mass transit down people probably weren't able to even get in to handle snow/aircraft, etc, ad nauseam. Ultimately it was probably a case of not being to get an airplane off a gate more than anything else.
One would think CBP would be able to design a procedure around not being able to get an aircraft on an international gate but I would be surprised if even they weren't horribly short staffed, in which case it simply may not be feasible to design a procedure to handle.