Whatever benefit SS's direct to door service offers is FAR outweighed by the almost certain delays in getting to your destination.
Better to take the airport express bus
http://www.nyairportservice.com
into Manhattan (and switch to a cab if necessary) or a public transit option or if arriving on a Thursday or Frday look at the Hertz/Avis 1 way airport->Manhattan airport special rates.
also, iirc, the airport bus does make stops at midtown hotels.
Even my mother, who LOVES Super Shuttle has now changed her tune after the literally 3+ hr trip from JFK to the East Village.
Unlike trips TO the airport which IS a viable option, FROM the airports, Super Shuttle has no set departure time.
Worse yet, since they make you wait for enough passengers (going anywhere in Manhattan or lower Bronx). they then lock you into a meandering and traffic filled multi-hour extended tour of the city.
please please please...find another way and enjoy your visit