This is the first I've heard of buses to JFK only. Yet, even if a bus to LaGuardia were available, the cost would likely exceed that of a taxi. We've always made our transfers by taxi... usually US$35-$45 total.
Note that waiting for a taxi at the New York Passenger Ship Terminal can be long. We've found that we could get a taxi much more quickly by walking out of the terminal and heading east. We've always found a taxi within one block.