Marisa Aragon's lapel pin is for the 54th precinct which is Esposito's old precinct (from "Den of Thieves").
At the beginning of the episode, as Beckett and Castle approach the crime scene, they compare themselves to other crime-solving couples, and Beckett comments that Castle "still reminds" her of Hooch from Turner & Hooch (1989). She first makes a comparison between the two in "Deep in Death (2009)".
The geo coordinates provided in this episode (40.675928, -74.043152) actually correspond to a location in the Hudson river, just south of the Statue of Liberty.
Gates says Stone used the pay phone to call an unknown person in the Maldives. When asked who it was she replies the cell phone he has is no longer active.