For the sake of completeness I saw this hanging around at the bottom of the page....We took Taxi/Ferry/Hotel Shuttle combination and was remarkably easy.

Taxi went over the Triborough Bridge, across to the Henry Hudson and straight down to 39th St Ferry Terminal. Ferrys were every 20mins and called the hotel shuttle which we waited about 10mins for at the other end.

Taxi cost $30
Ferry cost $6 pp
Hotel Shuttle free

^

We were in Midtown the second night and caught a taxi straight back to LGA. $30 again.