I find that incredible story of photographers who claim they were detained by police in Bayonne, NJ, to be an outrageous violation of civil rights.
First of all, being a retired police officer myself, in this day and age any police officers who would knowingly violate a person's civil rights -- even under the guise of heightened security -- have left themselves open to a personal lawsuit. Your rights were violated in the following ways:
1. Being detained for over an hour without breaking any law
2. Having your personal property destroyed (your photographic images) by coercion
3. The threat of taking your personal property (camera) without a warrant
4. The mention of taking you someplace for further interrogation without any probable cause
You say you are not a citizen of the U.S., but you are still under the protection of the U.S. Constitution. The least you can do is file a complaint with the Bayonne Police Dept. and N.J. Transit. Also, I don't know your country of origin, but I would notify the Embassy and file a formal complaint with them. Most importantly, I would contact the newspapers -- your best bet would be the Newark Star Ledger. I'm sure they would be very interested in your experience.
The worst thing you can do is nothing.