And, as CBS News Correspondent Bob Orr reports, patrols are constantly watching for boats approaching any of a hundred possible terrorist targets like bridges, the Statute of Liberty and the ferries which carry more than 19 million passengers a year.
"Where before it may have been perceived as a tourist, now we consider any sort of concern - we respond," says Lt. Craig MacLennan, of the U.S. Coast Guard
Inside the U.S. Coast Guard's camera control room, 17 surveillance cameras keep a round-the-clock watch on the harbor. And computer profiling and intelligence information enables the Coast Guard to zero in on possible threats.
Last September, a container ship was quarantined when sensors picked up signs of radiation. Only after inspectors traced the radioactivity to ceramic tiles was the ship permitted to enter New York.
"By identifying the vessels, the owners and the cargoes, we're able to target our inspections and examinations," says Capt. Craig Bone, of the U.S. Coast Guard.
In part, port security can be measured by things that haven't happened. Since Sept. 11 there have been no terrorist incidents in U.S. waters. And the captain of the Port of New York says he has no doubt that interventions have prevented some attacks.
That prevention effort doesn't stop at the water's edge.
Chief Customs Inspector Kevin McCabe says 90 percent of his resources now are aimed at stopping terrorists.
"Before Sept. 11 the contraband was almost always narcotics," he says. "Post Sept. 11 the major focus and almost the primary focus is definitely looking for anti-terrorism type targets, weapons of mass destruction or components of weapons."
Highly-suspect containers are checked for radiation and run through giant X-ray systems to help inspectors spot any sign of danger.
So far, none has been found. But for Customs and the U.S. Coast Guard, the terrorism watch goes on.
"We're going to have a threat here for years to come," says Bone
Standing just across the water from ground zero, no one needs to be reminded of the risk.