The only one that comes to mind is SuperShuttle. I just looked at their Web site -- one-way fares for a party of 2 between the airport and Manhattan cruise terminal start at $26 (LaGuardia), $35 (JFK), or $32 (Newark) for a shared van service. Again, this is for two people. There's a fare quote area on their Web site if you want to take a look at what they offer.
Compared to a taxi, these prices are pretty good. The downside, though, is that you might very well have to wait for the shared van to fill up.