Where in Manhattan are you going? Options are:
-taxi; $50+tip anywhere in Manhattan
-NYAS bus to Grand Central-42nd & Park Ave., Port Authority-42nd & 8th Ave. (Times Square area) or Penn Station-33rd between 7th & 8th Ave.; $15.
-Airtrain to Jamaica Station, LIRR to Penn Station. You can take the subway at Jamaica Station (E or J) or Howard Beach Station (A) but I wouldn't call it comfortable, but it's cheap and will take you pretty much anywhere in Manhattan ($7.25 including Airtrain fare).
Where in Manhattan are you