Getting inside metro tunnels isn't as easy as entering the police department or movie studio. After advancing in the storyline you will be able to use the elevator shown on the pictures above. It can be found in Adams port in the southwestern part of Founders' Island. Once you reach the elevator, you must attach to it with the winch and by loading the generator make the elevator move.
Important - due to the bugs in the game the elevator sometimes doesn't move after loading it with the winch. In that case you must ride inside again and position the Batmobile in different place.
If you want to leave the metro tunnels, go back to the elevator and use the winch again.