I'm not a lawyer.
You'll probably not have any success with a class action lawsuit. First, the city is pretty good at preventing itself from getting sued. Secondly, New York has specific rules about class action lawsuits - they're for consumer products only, and subject to a bunch of regulation.
Secondly, I don't think we're going to get much traction from the "discrimination" argument. Motorcyclists aren't a protected class (like the disabled, racial minorities, etc.) and we don't have a "right" to "access" things like parking spots. The Muni-Meter system is stupid, wasteful, illogical, and ridiculous. It's utterly foolish that they don't accommodate bikes and scoots. But it's not illegal.
You could theoretically sue the city for the time and effort it takes to fight every...single...stupid... Muni-meter ticket, but unless you have a family lawyer on retainer, it's a bit of a waste.
Your ticket is handled by administrative law judges who operate outside the real legal system and their practices are controversial. http://www.nyc.gov/html/dof/html/parkin ... peal.shtml
My guess is that the best route to deal with this is by appealing a ticket if you don't prevail in your first defense. There is an appeals board to deal with what the ALJs have screwed up. Those hearings are held in a "article 78 proceeding" which is a forum for dealing with these extra-legal situations. I don't know what the success is in getting (1) a reversal of a bad ALJ verdict, and (2) having that info trickle down to the other ALJs or NYC to prevent the future ticketing of bikes. Or fix the Muni-Meter system.
Others can chime in but this is my general understanding of the situation.