[eggy]

Motos emit less CO2, but more NO, however, most motos are now adopting the EU emissions standards with Euro 5 for motos, so I think that gap is not as bad as when Myth Busters did their episode on it.

Motos are certainly less congestive especially with most cars being single driver and no passengers going into NYC.

[Jolter]

If you do the math on the CO2, the emissions per passenger mile is significantly worse for a motorbike than for subway or bus -- regardless of the power source for the train or bus.

But, again, I don't think this proposed fee/tax is aiming at pollution or carbon emissions per se, more at the congestion itself.