The designation is the federal government's highest level of recognition for a historic site. The lighthouse, authorized by Congress and President George Washington in 1792 and built in 1796, has been on the National Register of Historic Places since 1969.
There are more than 86,000 sites on the national register. But there are fewer than 2,500 National Historic Landmarks.
Interior Secretary Ken Salazar approved the upgrade in March, and the ceremony on a meadow below the beacon Wednesday made it official.
Rep. Tim Bishop (D-Southampton) called the designation "a story of the power of a collection of people coming together to make something happen."
It took the Montauk Historical Society, which owns the site, more than six years to obtain the designation. Even the distinctions that Montauk Point was one of the nation's first lighthouses and that the first president commissioned it wasn't enough to garner the honor.
The application was twice denied because supporters hadn't proved the structure had an exceptional role in "interpreting the heritage of the United States," as federal guidelines required.
So society lighthouse committee member Eleanor Ehrhardt and historical consultant Robert Hefner used the Internet to find shipping records and other data to detail the lighthouse's role in the development and growth of the Port of New York, the busiest in the fledgling United States.
They documented how the light became a critical waypoint in guiding ships coming from Europe between 1797 and 1870.
Even before there was a lighthouse, Native Americans set fires on top of what was called Turtle Hill to guide their fishermen's boats back to shore.
Dick White of the lighthouse committee noted that 2 million visitors have seen the lighthouse in the 25 years it has been maintained by the historical society.
National Park Service historian Robie Lange, who presented the plaque to Ehrhardt, said the designation would make the lighthouse eligible for federal grants and tax credits.