Originally Posted by
jbcarioca
There ends out being minimal difference between these two in my experience. I just take the first train and ignore direction. If speed matters and you're to be close to Penn Station the LIRR from Sutphin Blvd/Jamaica is far faster and slightly more comfortable too, with fewer stairs for schlepping bags.
The split on the subways is around West 4th Street. North of that you're better off on the E (especially on weekdays when it is express in Queens) and south of that the A train is generally better. And I think the A station at Howard Beach is nicer than the Sutphin station. Just the one set of stairs down to the tracks rather than the split levels and such.
As for time savings by switching between the tracks on the loop, it is probably a 10 minute loop total. If the inner loop train is arriving at the same time as you get to Terminal 1 you end up saving ~7 minutes. If you end up waiting too long on the platform for the other train to show up then you will save less time.