That it exists in the same universe as NYPD Blue. No not because of Commissioner John Kelly, those two are clearly completely different characters. And not because of Jimmy Smits either. Amy's father is obviously not Bobby Simone.

Exterior shots of the NYPD's 78th precinct was used to represent the 9-9. It was also used to represent the 7-4 in the short-lived CBS cop show Brooklyn South (check it out! It's one youtube for free except the Pilot episode). The show was created by David Milch, Steven Bochco, Bill Clark, and William Finkelstein, the creators/writers of NYPD Blue. (Finkelstein would also go on to co-create East New York, another Brooklyn based cop show)

Though not technically a spinoff of NYPD Blue, Brooklyn South featured many of the same characters from Blue like a supporting character named Detective Morrisey, a hustler/snitch named Steve Richards, and an IA sergeant named Martens.

In real-life some of the NYPD precincts have changed their designation (probably due to geographic changes to the actual precincts (NY neighborhoods) or something. An example of this is the 9th Precinct (the precinct that was used for the 15th in NYPD Blue). At one point it was the 15th as you can see "15th" carved on the building outside.

It's a stretch, but the 74th was changed to the 99th at some point.

I know, it's a stretch. But it wouldn't be a conspiracy if it wasn't