Plot hole: Amy lets Scully place the watch in the break-room, but how could she have known that after Captain Holt steals the crown out of the locker, he would go there? And not, for example, go back through the window he came from.
Other mistake: Holt takes the crown out of the back of Jake's cabinet. However this wouldn't be possible as the crown was in the top drawer. This would have a back on it and it wouldn't be accessible by just removing the back of the cabinet.
Answer: In reality, the Commissioner is a civilian administrator, appointed by the mayor of New York City. He (as of this writing, the role has always been filled by a man; the show gets that part right) is usually someone who has risen through the ranks of the NYPD, but upon becoming Commissioner, is no longer a sworn member of the force (the highest sworn rank is that of Chief). Since Commissioners are appointed, technically anyone can serve in the position, including Deputy Commissioners (who are appointed, in turn, by the Commissioner himself).
Update: On 1 January 2022, Keechant Sewell became the first ever female commissioner of the NYPD.