I've done it three times with three different cruise lines and never had a significant line or wait ( 20 minutes the longest) . That said I can't comment on changes since 9/11.
My guess is that security is much tighter. Last May we walked on to the ship with NO
security scan of any kind (carrying all our luggage). It has to be different now. Trip from LaGuardia can take 20 minutes and can also take well more than an hour . Depends on day of the week , time of day , accidents and construction.