According to the script, you are mistaken, the Doctor does not say New York is unique
RIVER: It's like they've taken over every statue in the city.
DOCTOR: The Angels take Manhattan because they can, because they've never had a food source like this one. The city that never sleeps. (Slow heavy footsteps outside the window.)
He is saying the Angels have never had a food source like New York, not that New York is unique. The statement does not say they couldn't have chosen Tokyo, or any other city - but for the angels a highly populated bustling city is a new experience. it just so happens they chose New York