I have minimum familiarity with subways...friend asked this question.
What is the best/fastest method subway travel Mid week around 4-5pm from Coney Island to LIRR,, Is it to Altantic ave or Penn. and what sub line is best. Does the LIRR connect with subway at Atlantic ave.

In comparing the two maps, it doesn't look like there is much of an easy way to get from Coney Island to LIRR. In Brooklyn, the LIRR stops at Flatbush, Norstrand, and East New York.

From what I can tell the closest common connection between the two is Norstrand. But you're looking at probably two trains and a shuttle transfer.

You could probably take the Q to Prospect Park, then take the shuttle from there to Franklin Ave. One stop on the C train from Franklin Ave is Norstrand where you can pick up the LIRR.

Perhaps someone knows an easier route? I just came up with this from comparing the two maps.

Take the Q or D to Atlantic Ave. which is also the LIRR Flatbush Ave. stop

Schedule is here:
http://www.mta.info/lirr/html/ttn/flatbush.htm

Take the Q or D to Atlantic Ave. which is also the LIRR Flatbush Ave. stopI think the N train stops there as well - so you can take any train EXCEPT the F from Coney Island to Atlantic Av (Pacific St) and pick up the LIRR there.

Travelling all the way to Penn Station to catch the LIRR is just waste of time. I used to work in lower Manhattan, and many people would actually take the IRT subway (2/3/4/5) from there into Brooklyn to pick up up the LIRR rather than heading uptown to Penn Station.

Note that the stop on the D and N is called Pacific, not Atlantic (on the Q it's called Atlantic). But it's all the same station, and it is indeed connected directly to the Flatbush LIRR terminal.

The D and N are express in Brookyn, and therefore probably a little quicker than the Q.

I agree that it's a complete waste of time to go to Penn Station. Even if you have to switch in Jamaica to get from Flatbush to your LIRR destination, the change in Jamaica is usually quite painless.