Taxi would be best, $45+tolls+tip for the both of you direct to the hotel. There's the Airtrain-to-subway option ($7.25 per person) however this would require at least one subway line-to-line transfer along the way. Depending on where your hotel is on 94th St. there are three 96th St. subway stops on multiple lines; the #1, 2 or 3 subway at Broadway on the west side, the C subway at Central Park West and the #6 subway at Lexington Ave. on the east side. There's also the NYAS shuttle bus ($15) from terminals to Grand Central Terminal where you can access the #6 subway or Port Authority Bus Terminal for the C and #1, 2 or 3 subways.
Taxi would be best,