Turns out that this guy has shaken his FBI handlers and that's appropriate since his street name was 'Nicky Shakes' and he's in town to discuss a book deal. But a whole lot of people are keeping tabs on him even if the FBI has fallen down on the job. It's why he winds up dead.
The guy who has the most to gain with the deceased's demise is Frank Savino who is a Mafia Don putting on a crazy act. See how Dr. Skoda gets under his skin.
Who actually does the deed is a bit of a surprise, but the motive is completely understandable.
A great Law And Order story.