Revealing mistake: When Charles shows the picture of the horse and says "look what you get when you search for 'Charles Boyle medal of valor'" he's typed "peanut butter the horse" into his phone.
Revealing mistake: When the motor home explodes, the flames from the explosion are CGI. It doesn't look very realistic at all.
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.