There may be a "This guy is from Out of Town and I'm charging him an extra $5" fee, but other then that, there is no surcharge for anyplace in Manhattan above the $35 plus tolls.
Not to say they won't try to get you for it though, I met a woman in the TKTS line a while ago who couldn't believe we charged $35 per person for the four of them to get from Kennedy to Times Square.
She wasn't happy when told that isn't the case, as she forked over $120 (he gave her a $20 cash discount) for the ride.