(1/)2/3 to LIRR is definitely faster than taking the E train, by at least 15-20 minutes. Via LIRR it's almost always one hour door to door, from the 72nd St station. However, E train is obviously quite a bit cheaper ($7 less I think at this time).

The other issue with the E is that apparently some E trains during rush hour don't go to the Jamaica LIRR/Airtrain station, but instead travel along the F line. I found this out the hard way a year or so ago. That added another 20 minutes or so as I had to back-track. I felt like such a tourist.