Oil processing is definitely bad for the environment, but think for a moment about the scales. Just in raw materials, ignoring the massive impact of battery manufacture alone, the average motorcycle weighs less than 600 pounds. The Prius weighs about six times that. That means six times the amount of shipping, forming, refining, finishing, et cetera…
The Prius still has an internal combustion engine that burns gasoline, and requires a significant amount of rare-earth minerals for the construction of its catalytic converter. Most motorcycles now have catalytic converters, but they are smaller and thus the environment suffers less damage per vehicle.
I agree that a Prius will burn cleaner while running than probably any motorcycle – but the total amount of damage done just by being built has to be a whole lot more than almost any motorcycle and it can’t be close.