Well that's the comicverse explanation of the cities. Metropolis is said to be the nicest part of Manhattan at noon on the first day of Summer with the nicest weather possible. Gotham is the worst parts of NYC, at midnight on a new moon on the first day of Winter.
But in "reality" both cities exist in the same universe, are separate cities, so they must both exist in different places.
But in "reality" both cities exist in the same universe, are separate cities, so they must both exist in different places.