Coast Guard Petty Officer Frank Iannazzo-Simmons says the whale was spotted around 8:00 a.m.
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The Coast Guard put out an advisory telling mariners to watch out and avoid contact with the whale. Boats of all sizes frequent the area, including Staten Island ferries and cargo vessels.
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Dr. Howard Rosenbaum at the Wildlife Conservation Society says the whale was likely a humpback, which stay close to shore between Fire Island and Brooklyn and are most often seen by people.
"We have some of the largest animals on the planet in our own backyard. It's a reawakening to New Yorkers of all the amazing marine life in our waters," Rosenbaum said.
Rosenbaum said it's likely the whale was feeding in the area because there is a lot of prey, such as Atlantic menhaden (bunker) fish, right now. Thousands of the those fish turned up dead in a Long Island canal earlier this week.
"The large school of fish was most likely chased into the canal by other predatory fish," the DEC said in a statement.
While the humpback whale is most often seen, different species of whales have been spotted or detected with increasing frequency in New York waters near the Verrazano-Narrows Bridge and just off the coast between Long Island and New Jersey in recent years, but Rosenbaum said it's not often one is spotted in the harbor.
While it's an exciting time for those who study and those who enjoy watching whales, it's also a challenging one.
"We're concerned about (whales) being hit by ships and the noise in the area," Rosenbaum said.
The Wildlife Conservation Society is working with the Hudson River Foundation, the shipping industry, federal, state and local officials among others to learn as much as they can about whales in the area waters and why they are here.
The WCS and the Woods Hole Oceanographic Institution deployed a detection buoy just outside New York Harbor over the summer to monitor the presence of baleen whales in near real time by automatically detecting and identifying their calls.
Just this week the buoy picked up a highly endangered North Atlantic right whale in New York waters. Only about 500 North Atlantic right whales left in the world.
Rosenbaum says the buoy has also picked up the presence of fin whales since June, including every day in November. A fin whale is the second largest animal on the planet. The blue whale is the biggest.
You can learn more about the buoy, nicknamed Melville, at blueyork.org/whales