Someone posted this a while back. Sorry, I can't remember who. It's from the comics, of course, not the show, but it's still handy for filling in location blanks that the show never mentioned for Metropolis. As you can see, it mentions Stryker's Island Penitentiary, as C_A says. And, since it also includes locations such as Centennial Park, mentioned in LNC, you probably couldn't go wrong assuming some of its other locations work for the show when you're writing a fanfic.
Map of Metropolis An island prison, an Alcatraz type of thing, was, I believe, mentioned in one of the published LNC novels. Can't recall which one. Have a feeling it was the awful Cherryh one. Lois went on a ferry, I think, to visit Luthor there. Although I'd take that with a pinch of salt - my memory's really hazy on the details.
LabRat