What is the best way to go to Brooklyn, court street from Ronkonkoma long island. LIRR goes to Jamaica, Penn and Flatbush, but I would like to know which one would be the best station to get the train for Brooklyn from these stations.

It's pretty easy. Get the LIRR to Atlantic Avenue and pick up the subway. Take the Manhattan-bound 2, 3, 4 or 5 to Borough Hall.

Take the train to Flatbush (that's in Brooklyn). Go outside and walk along Atlantic Ave to Court Street (4th Ave, 3rd Ave, 2nd Ave, Smith Street, Court Street - something like that).
That should save you a subway fare.

Note the LIRR use to go down Atlantic Ave, but that was in the 19th Century.

You could have been nice and said the 20th Century!

Sorry, it's been a while.

I think the responder means that the LIRR used to go down Atlantic Ave in the 19th Century prior to Brooklyn bec oming incorporated in New York City.