Another photographer was harassed at Penn Station. He was arrested and hurt by the police officer during the arrest - here is a link to his post about the incident.

He has written letters to Amtrak posted here and here

A summary of the incident is in the second letter:

I'm writing you as a result of my experiences in Pennsylvania Station New York on December 21, 2008 at about 12 noon. I had taken New Jersey Transit Train 7826, departing New Brunswick Station at 10:58 and arriving at Pennsylvania Station New York at 11:52. I was in the 2nd to last car of the train which dropped me off on the western end of the platform for Tracks 9 and 10 in Penn Station. At no time prior to 5PM on December 21 was I east of the escalator that is immediately east of elevator B5.

I am an amateur fine art photographer and take photos of subjects I see. I was starting to work on a submission for the "Picture our Train" annual contest which has been run for the previous 5 years. In the previous announcements of the contest there is a section "Safety First". In this section it states "Stay in public access areas such as stations, sidewalks or parking lots." So after detraining I wanted to spend a few minutes taking some photographs from the platform.

To get to the platform I did not cross any barriers, did not see any "No Trespassing" signs. I did not pass through any closed doors. I was about to exit the platform at just after 12:01 PM by using the Escalator that is just east of Elevator B5. At this time I was approached by Amtrak Police Officers Rusbarsky and Smith. They asked me what I was doing on the platform; I answered taking photographs of equipment. I had an email from New Jersey Transit that says photographing is allowed from all publicly accessible areas of New Jersey Transit Property and photo ids are no longer needed which is the service I use to get to Pennsylvania Station New York. I showed the paper to Officer Rusbarsky. He stated this is Amtrak not New Jersey Transit. They asked to see my tickets, I showed them my New Jersey Transit Tickets, of course the one I used to ride into the station on had been collected on the train. Officer Rusbarsky then wanted to see the photographs I took. He then demanded that I delete the photographs. I refused to delete my photographs. They also said did I see the "No Trespassing" signs, I asked, "what signs?" and looked around for one. I was then arrested for Trespass NY Penal Code 140.05.