If we are arriving at Penn Station from out of town and need to get immediately to JFK at evening rush hour on a Friday, is the best bet the Long Island Railroad and Air Train combination?

Sounds good to me.
As long as there are no delays on the trains, you should be fine.
When do you arrive Penn Sta and then have to be at JFK for your flight?

Well this isn't set in stone. We'll be in the city for a month, then may take a train up to Providence for a few days to work with friends/clients on Buzzard's Bay. Our flight to London is out of JFK in the morning, so I'm thinking take the train back to the city from Providence and then on out to JFK for the night (free night at Marriott Courtyard, perhaps), so we're there by 6:30 the next morning.

Most definitely. Some trains are quasi-express & others stop at:
Woodside, Forest Hills, Kew Gardens. Max train time should be
about 23 minutes. Sit near front of
train to get off & take escalator
up to AirTrain & Determine your
terminal before boarding AirTrain
'cause some brilliant folks did not
think to post this info in the actual
cars.

We took the Air Train to JFK a couple weeks ago, and the terminals for the various airlines were clearly posted in the car. Instead of taking the LIRR, we took the subway to Jamaica Station instead (E line), and it was very easy and convenient.

I wish I had checked this before I left for New York! I asked one of the MTA workers at the subway booth about how easy or difficult it was to use the subway from 50th street to get to Jamaica station and to transfer to the Air Train. I figured with having another two days of subway rides already paid for why not just pay the additional $5 per person to ride the Air Train to JFK and save the $79 plus tip the hotel wanted for their shuttle service. However, the MTA subway person told me if I had luggage it would not be the best idea. I asked if there were lots of stairs or if there were also escalators once we got to the Jamaica Station and needed to transfer. She said there were LOTS of stairs and no escalators or elevators so I would probably prefer the shuttle service. Apparently I was misinformed about the escalators from her!! That was an expensive $90 trip back to the airport that should have only cost me $5.

I have taken the Airtrain twice now and it works very nicely. There are many LIRR trains that stop at Jamaica and then it is a ten minute ride to the furthest terminal.

karentoft, even a TAXI is a set fare of $45 plus possible toll ($4) plus tip or max of $60. How did you pay so much for a "shuttle"?

Btw, what you were told is not incorrect. This thread started with discussion of taking the LONG ISLAND RAILROAD from Penn Station which sometimes does require stairs when you transfer at Jamaica.

The $79 plus tip was from my Manhattan hotel back to JFK. There is only a flat fee to get into the city not back to the airport.

That is no longer true. It is now a flat fare of $45 (plus toll) BOTH to and from JFK to anywhere in Manhattan.

from http://www.nyc.gov/html/tlc/html/pas...cab_rate.shtml

Flat Fare from John F. Kennedy Airport:

The Taxi & Limousine Commission is conducting a "Flat Fare" program for trips between (to and from) the Borough of Manhattan and John F. Kennedy International Airport.

The flat fare is $45.00 plus any tolls. The meter will not be turned on and the night surcharge will not be added.

If passengers request multiple stops, the flat rate of $45.00 will be collected at the first stop in either Manhattan or John F. Kennedy Airport, and the meter will be turned on for the remainder of the trip. The metered fare should be collected at the last stop, from the last passenger.

For $79 you should have gotten a real limo (like stretch caddy or Mercedes - or you were robbed).

OK, I still find this a little confusing.

If I'm at Penn Station, to get to JFK I can either:

Take a LIRR train to Jamaica and take Airtrain from there to JFK

or

Take the E subway to Sutphin Blvd-Archer Ave and take the Airtrain from there to JFK.

Is one cheaper, faster, easier with luggage than the other? Depend on time of day? Subway bad at rush hour with luggage? It seems the LIRR does cost $5 more.

The subway option is ~ $5 cheaper than the LIRR option. LIRR price varies slightly depending on time of day. The LIRR is on the same level as the AirTrain so switching with luggage is easier and it's reportedly also faster than the subway partly b/c of fewer stops. When you use the subway, you will need to do stairs at least to transfer to the AirTrain.