some NYC garages (manhattan anyway) do offer discounts to smart fortwo owners, some discounts amount to 1/2 price, some to motorcycle rate, some offer a flat rate. never hurts to ask, if you have a location in mind. let them know that you know that it is a pretty common practice.
if you do, try to get a garage that already has a few smarts parking there.
treatment of the car and of the owner (eg. customer service) are separate issues from price.
smart center manhattan should have an up to date list and details.
I've dealt with three garage brands since 2008, all in Manhattan, with different pricing / location / service combinations.
you could do worse than to start looking here: http://www.iconparkingsystems.com/icon-green/smart-car/
but the page seems not to be loading right now. maybe by phone: (877)PARKING