Bounty targets spawn in the areas of the side mission that get blocked off. I managed to kill all the bounty enemies to progress it, and it only lead them to spawn downstairs, where the elevator doesn't work.
https://imgur.com/tBgs1Nc
https://imgur.com/C6MEHrA
Elevator has no prompt, Broken elevator door has no prompt. Unless they spawn near the boat, bounties in this area are impossible.
I have completed the New York Federal Reserve side mission.