Whether this is better depends on where you're going. All the tunnels are open now, so traffic is not too horrible (at least no more horrible than before Sandy). But it's still often pretty bad during the busy part of the day. Normally, the combination of Air Train/LIRR takes about 35 minutes from terminal to Penn Station, but with the reduced LIRR schedules it might take a bit longer (say up to 45 minutes). The Air Train to E train takes no less than 45 minutes and sometimes more depending on where you're going.

Fares: The fare for the LIRR varies depending on when you're getting the train. 2:30 is off-peak, so it's $6.25 (as long as you buy your ticket before boarding the train) + $5, so $11.25 each (it will be just $8.75 on Sunday because you can use a "City Ticket". The subway is always $5 + $2.25 (as long as you buy a regular Metrocard; it's $2.50 if you buy a single ride). So always $7.25 or $7.50.

However, the taxi fare is fixed at $52 plus tolls plus tip for about $65 to $68 (not $60, so the round-trip is a bit more than you originally estimated).

I prefer to take the Airtrain and Long Island Railroad combination, but those trains are running very full and somewhat off schedule now, so the E train might be your best choice.

Do the E train if your hotel is within 2 or 3 blocks of an E subway stop (53rd/Lex, 52rd/Fifth, 50th/8th/ 42nd/8th). Take the Long Island Railroad if your hotel is closer to Penn Station (I'd do that over the $ even if my hotel were close to 34th/8th, which is an E train stop).

Realize that if your hotel isn't close to an E train stop, then you will have to transfer to a different subway line or take a taxi, both of which can be a pain.

Hi Doug,
Good call, I did forget about the tolls so that is even more reason to take the Airtrain and LIRR. I think we will be taking the LIRR about 3:15 or so. My place is about 2 blocks from the 50th/8th stop so the E Train may be the best bet.

Taking the subway is fine as long as you are prepared to haul your luggage up several flights of stair, which may be steep and narrow - and are often crowded.

It you wife can carry her bag fine. If you have to deal with both bags at once - that could be an issue. Can the bags be carried?

If they are both wheeled bags you might be left trying to haul both up a stairway - one on either side of you - with the potential of blocking other people trying to run up and down the stairs. (I have seen someone try to maneuver 2 wheelies down the street - one in either hand - and they were really clogging things up. Naturally both wouldn't pull exactly the same way - so this person was walking extra slowly and taking up the space of 2 or 3 people side by side. And people rushing for a train were not pleased.)

So if you are sure you can manage the bags go for it. There is no problem with safety - but do make sure that you are hanging onto your bags at all times in the subway. And don't put them in the doorways.

Caveat: I am long past the age of being pack mule woman and always take a cab or car service when I have luggage - although I ride the subway all the time without.

Thanks ny traveler! My wife and I are young and able and capable of each carrying out own bag plus a carry-on I'm sure.

Fortunately our bags can be carried so it shouldn't be too big of an issue.