Such a permit is needed for the construction and operation of electric transmission lines at the U.S. international borders.
The 1,000 MW Champlain Hudson Power Express transmission line has been in development since 2008.
The project is aimed at saving about 2 percent to 3 percent on energy bills in New York City. The developer has said ratepayers also will see price breaks from Long Island to Albany.
The line will run under the length of Lake Champlain, through parts of the Hudson, Harlem and East rivers and beneath railroad rights of way from Quebec to Queens.
Construction is expected to take about four years.