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AFAICT there are highways affected by this congestion charge. Federal Highway Administration's Value Pricing Pilot Program [1] is the means for state/regional/local governments to institute programs like this. The specific signoff was for an environmental assessment [2] showing that the proposed program complies with relevant environmental laws.

[1] https://ops.fhwa.dot.gov/congestionpricing/value_pricing/ind...

[2] https://new.mta.info/project/CBDTP/environmental-assessment

42nd Street between the Midtown and Lincoln tunnels is part of I-495. That's why the last exit on the westbound LIE is #15, Van Dam street. Exits 1-14 are the avenues from the west side of Manhattan (where the numbers reset because 495 crossed a state boundary) to the east side. If you look carefully you will see I-495 signs on some streetlights or traffic lights.

Because there are Federal highways in the impacted zone.

In addition to other reasons given, the big one is interstate commerce.