Q. What is it supposed to be on the show?

A. A prison.

 
Q. Where is it supposed to be on the show?

A.  Based on a brief establishing shot, this is probably supposed to be Rikers Island prison, in New York 

Q. When did we see it on the show?

A. We first see this prison near the end of Episode 5 of Season 1 of Resurrection, when Charley goes there to talk with Mia (“Lady Vengeance”), who has been arrested thanks to Dexter turning her in when she was about to kill an innocent man. Mia assures Charley that she knows the rules and doesn't plan to do anything stupid, but Charley issues what sounds like a veiled threat, saying that they will make sure that Mia's time behind bars “is short”.

We see the prison a second time in Episode 6, when Angel Batista joins NYPD detectives Wallace & Oliva in visiting the prison, with the intention of talking to Mia and showing her a photo of Dexter, to see if she knows him. But when they get to the prison, an alarm sounds and they find the body of Mia hanging in her cell, an apparent suicide.  They take her body down and she is pronounced dead by a prison guard.


But that prison guard turns out to be the same man that Charley bribed in a gambling den, so it is strongly implied that Charley arranged with the guard to have Mia killed in her cell, to ensure her silence .

Q. What is it actually in real life?

A. Surprisingly, this scene was shot in a real-life prison.

The vast majority of Hollywood's prison and jail scenes are filmed on studio sets. In fact, in Los Angeles there are a number of fake prison sets that can be rented for filming.  So it's rare to find a scene shot in an actual prison.

Q. Where can I find it in real life?

 
A. This prison scene was shot in the Nassau County Correctional Center, an active prison which is located at 100 Carmen Ave, in East Meadow, New York. 
 
That is on Long Island, but is located far south of the two Long Island mansions, and far east of the Long Island locations where Dexter follows the Dark Passenger Killer.    

Although the Correctional Center houses many convicts, this particular building where they filmed the scene was decommissioned long ago, and now sits empty -- which makes it available for filming.

The IMDB reports that the 1972 film “The Hot Rock”, starring Robert Redford, was shot at this prison, as well as several lesser known films, and I've been told that they also filmed episodes of “The Good Wife” and “Person of Interest” here.



( They did, however fake the brief establishing exterior shot of the prison, that is shown right before Batista's visit. That image actually is actually just stock footage of Rikers Island prison, which is about 20 miles NW of where the scenes were actually filmed. )
 
 
Here is a StreetView of the actual prison building : 
 
 

Here is an aerial photo of the location.  And here is a map link.