Dexter receives a mysterious phone call from Charlie saying that Prater has a surprise for him , that he should come to Pier 6.
When he shows up there, he finds a helicopter waiting for him on the pier, along with Leon Prater and Rapunzel Al Walker.
Prater says he thought this would be a nice change of pace, but when
they get in the copter, he waits for the arrival of Gareth, The Gemini
Killer.
However, Dexter knows that Gareth won't be coming, because he killed him, after he found him waiting inside his house.
So it's an understatement to say
that Dexter is surprised when a car pulls up and who other than Gareth
gets out and heads to the helicopter.
The truth suddenly dawns on Dexter: The Gemini Killer is actually a set of twins. And this one is still very much alive.
We see this heliport once more, in episode 7, when the group returns (minus Gareth) after dark.
Q. What is it actually in real life?
A. A heliport.
Q.
Where can I find it in real life?
A. This is actually the Downtown Manhattan Heliport, which is located on Pier 6 of the East River, in the Financial District of Lower Manhattan (not to be confused with the Pier 6 in Brooklyn).
It maps to approximately 1201 East River Greenway, NYC, but the official address appears to be 6 East River Piers.
It's about half a mile southwest of the Seaport, where they filmed the scenes of Dexter stalking Gareth at the bookstore, and Harrison visiting the NYU booth.
And it's less than a mile southeast of the spot where Dexter took off in Prater's yacht in the season finale
As you can deduce from the name, it's an actual heliport, serving downtown Manhattan.(Reportedly, the President lands there when he's in town.)
I simply googled for heliports in New York, almost immediately found this Wikipedia article
about the The Downtown Manhattan Heliport, and then simply used Google
Earth to check out the location and make sure it matched what we saw in
the episode.