I suspect that this is due to the elimination of toll shopping/avoidance. Per [0] and [1], the only way to avoid a toll entirely is to drive from the West Side Highway or FDR Drive to the Brooklyn Bridge, but commercial vehicles are prohibited on FDR Drive and the Brooklyn Bridge has weight restrictions [2], so heavy trucks don't have a legal way to dodge the tolls anymore.

If you need to reach Long Island, the incentive to avoid the (tolled) Throgs Neck, Whitestone, Verrazzano, and RFK bridges are gone; now you're paying for the privilege of sitting in Manhattan traffic.

[0]: https://congestionreliefzone.mta.info/faqs

[1]: https://www.cbsnews.com/newyork/news/nyc-congestion-pricing-...

[2]: https://www.nyc.gov/html/dot/html/motorist/parkway-restricti...