Tax burdens are tough to pin down. For something like cruise ship docking, the fear is losing the docking business to a neighboring port. That can change ground economics for voting families, a problem for policy makers.
State or national-level regulation is probably needed.
Hoboken, New Jersey and Red Hook, Brooklyn are roughly the same distance from the city.
Would you as a person go on a cruise when you knew it contributed directly to the asthma of others? At that point, I think going on a cruise from a different port would be the preference of others, regardless of taxes.
Shore power works fine. It would be a lot simpler to just mandate it actually be used, and bar ships which don't use it from docking.
Later liquid battery tech could be a good way for a cruise ship to quickly refuel in port. Other grid-level battery tech might work too, but I'm actually not sure if a boat can cross the Atlantic on battery.
It seems that the externalities of this decision need to be accounted for in law.