Manhattan was an island and borough of New York City. Almost all of the Doctor's visits to the city were exclusively to this area. (PROSE: Salvation, AUDIO: Invaders from Mars, TV: Daleks in Manhattan, The Angels Take Manhattan)
John Kelly was a cat burglar from Manhattan. He broke into a museum to try and find a hiding place. (COMIC: Dr. Who's Time Tales)
UNIT had a base on Manhattan, which was attacked by the New Dalek Empire. (TV: The Stolen Earth)
While searching for the source of the Osiran energy signature, Erik Ulfriksson and Hanif studied a map of a part of Manhattan with Central Park and the Upper East Side. (COMIC: Spiral Staircase)
In Roma I, Marcus Americanius Scriptor's family home encompassed an elongated island between the Malum and Magnus rivers on the east coast of the Northern American continent. It was discovered during the reign of Romulus Augustus when three ships carrying salt from Africa were caught in a wind that carried them across the ocean. The island was around fifteen miles long and four miles broad. It contained a central park, several theatres, a marina, the largest atrium in the world, an underground railway, a tower that was the tallest in the world when it opened, and several renowned statues, squares, and galleries. In the bay south of the island stood the Jupiter Libertatis. 130 thousand slaves worked there maintaining the villa and tending its grounds. (PROSE: Warlords of Utopia)