I do not think that it is safe trying the 9/11 terrorists in New York City. They are terrorists and not war criminals, and do not have the same rights as those who would be considered war criminals. The 9/11 terrorists should be tried overseas away from New York just in case they escape.
Trying the 9/11 terror suspects in NYC courts would be a very difficult operation to undertake for forces of security, justice, and public safety. Transporting the suspects to the courts would be reason for a large increase in security in the area which would hinder the everyday lives of many in the area. Public safety would be at risk since many in America are still very upset and emotionally charged from the events and those individuals may act in comparably violent ways to instill what they believe is a more fitting punishment for the suspect's crimes.