The concept of a 'mafia', of organised crime in Metropolis planning their operations around Superman's comings and goings, goes back at least as far as the Silver Age.
The Silver-Age had stories where the city's criminal underworld were shown trying to be evasive and cautious about when and where it raised itself and took care of its business - Action Comics #267 is a good enough example as the tale shows how Lex Luthor arranges his operations and minions purposely to only strike when Superman is out of town or known to be focused on some emergency in Metropolis. The Bronze-Age had gangs like 'Skull' and 'Hive' active in and around Metropolis, I don't recall for sure whether they were monitoring Superman's whereabouts however....
Another example of the reality of Life in Metropolis for the criminal elite though can be found with Intergang in the early 1990's, where we are shown their modus too is to monitor Superman's movements and take full advantage when he is seen leaving the city or known to be elsewhere in the world - see Action Comics #653 for a prime example. Lex Luthor too was known to have a department specifically monitoring and reporting on Superman's movements early in the Post-Crisis years, something he would exploit to his advantage naturally.
I believe Rick Veitch's 2005 series 'The Question' featured a Metropolis Mafia and their methods of working underground, and around Superman's comings and goings.
So no, the concept isn't at all new. But Brian Bendis is the first writer to make it an ongoing plotline and have Superman directly faced with its existence in his city.
I believe it was that Question series you mentioned that I was thinking of.
Interesting that an "Invisible Mafia" of one sort or other has been around so long, I guess it would be necessary. Sounds like it might make a good ongoing story if handled right.