To get to the Ronkonkoma station by car, from the Lab take the William Floyd parkway south 2 miles to the Long Island Expressway (LIE), and go west to exit 60. The train station is about 1 mile south of the LIE from exit 60; follow the signs. There is am immense parking lot at Ronkonkoma, which is crowded during the week (due to commuters) but uncrowded over the weekend.
If you don't have a car, every Monday to Friday the lab has a car service which will take you to the Ronkonkoma station; it leaves from the travel office at 4:00 pm. Call travel, x2531, earlier in the day to reserve a place. Coming back from the City, the lab always has a car waiting at the Ronkonkoma station for the morning train. Check with the travel office for times, etc.
For driving tips to the City, go here and follow generally the tips to the Airports. It helps to listen to the reports on AM radio! Really!
The only difference is that you need to keep going into the City. Taking the Grand Central is always a good idea; cut to the Long Island Expressway before you hit Shea Stadium. The LIE goes right into the Midtown tunnel, but that is generally crowded and costs $3.50. The Queensboro bridge is free, gets you in on the upper East side, but is somewhat awkward to get to from the LIE. (There are signs from the LIE.) To get to downtown Manhattan, like Greenwich Village, from the LIE take the Brooklyn-Queens Expressway, BQE, to the Williamsburg, Manhattan, or Brooklyn Bridges. To get to Columbia Univ. and the upper west side of Manhattan, take the Grand Central Parkway up to the Triborough Bridge, and then take 125th street through Harlem. (Its ok, really.)
Parking in the City: YOW! Be careful of parking on the street. Its free, but the parking regulations are byzantine, and often very poorly marked. Also, there are tow services which operate like bandits. I STRONGLY suggest a parking lot, especially if you have a decent car. Parking lots can be expensive. You can often do well by going to the extreme west or east in Manhattan, and then looking for a lot. For example, on getting out of the Midtown tunnel, it costs $20/day to park. Go a few blocks east, and its $10. Parking at some random lot in midtown can be insanely expensive, like $20 for a few hours. Nuts. A little patience can be rewarding.
Parking lots run by the City are generally ok. Way downtown, off Houston by the West Side Highway is one for $10/day with a guy always there. Not covered, though.
Getting around the City: the subways are efficient and, if you have a map, easy to get around. They're also dirty, noisy, and hot in the summer (the cars are air conditioned, but not the stations themselves). Also, taxis are relatively cheap and relatively honest. Your main problem isn't taxi drivers ripping you off deliberately, but not knowing where to go, just having gotten off the boat themselves. If you have problems, get there taxi cab number, and make a big fuss. I never take buses, I can't figure out the routes.
One warning, however. On occassion we have had European tourists who think that impoverished Americans are somehow amusing; e.g., staying overnight in a homeless shelter. These people live the lives they do because they have no choice. If you go walking areas where people are obviously selling drugs or their bodies, and something happens to you, then it's your own dumb fault.
My favorite is Time Out magazine, which has an inclusive guide to everything, from theatre, to street fairs, to venues for popular music. It is limited for classical and jazz, though.
Also good is the Village Voice. They have an interesting selection of things to do, including theatre, dance, performance, and music. (By the way, the Voice is free in Manhattan, but costs everywhere else.) Also good is the New Yorker magazine, especially for jazz and theatre.
For places to eat, the standard guide is Zagat's, but be warned: the online version pales before the little red book. Besides the magazines mentioned above, also good for fancy places to eat is New York magazine.