To the best of my knowledge, the governor of New York absolutely does not have "special powers" over NYC. NYC's boroughs are normal municipalities for the purposes of state law.
You might be thinking of the MTA, which was formed as an independent state corporation after the city's bankruptcy. This is a source of persistent local funding headaches, but is not a "special power": the MTA's board is intentionally not fully appointed by the governor, to prevent exactly this kind of unilateral maneuvering[1].
I don't really think this has anything to do with remote work or RTO, etc., either. Congestion pricing was a pre-COVID policy that's been on the table for well over a decade; it's sound policy purely in terms of making the MTA financially sustainable and reducing congestion and air and sound pollution within Manhattan.
[1]: https://new.mta.info/transparency/leadership/board-members