Thanks so much for these tips. Poison Ivy - you are so right to suggest checking maps & YouTube videos, Penn Station is quite the busy place! Tthe maps & videos have helped.
Since we are coming from West coast, we plan to come a few days early to stay in NYC rather than just for the cruise, so will have larger suitcases. I checked the NJ Transit site, and at one place it says to travel light as there is limited room for luggage. What is 'limited space' and where does the luggage go on the NJ Transit train? I couldn't find a video that showed anything re the luggage. Want to be sure we can get on with suitcases larger than carry on size, as this does seem to be a very good option to get into NYC. Thanks.
The NJ Transit NE Corridor line is a great line to get to NY from NJ. Very convenient and very safe. I used to ride it all time to commute to NY from S. Jersey.
Here's the official site info provided for travelers connecting via the AirTran from EWR.
http://www.njtransit.com/rg/rg_servlet.srv?hdnPageAction=AirportConnectionsTo
Managing a suitcase on the NJ Transit line will take some ingenuity though depending on when you are taking the train. There is a small rack above the seats on both sides which can store a duffle/backpack but not a decent size wheeled bag. That would need to stay with you and the agents don't want the aisles blocked.
The Northeast Corridor line on NJ Transit (your train line to/from Newark Airport) is a major commuting rail line from NJ to NY. Most passengers won't have luggage during the weekday rush hour and it's not uncommon to have standing room only at certain points on those trains. But they run several express trains during that rush, which automatically bypass the Newark airport station.
So if you're travelling with a few bags in tow my first suggestion is to plan around off peak times when the trains are empty and you can easily spread out. Sat/Sun is ideal anytime or if it has to be a weekday, try to board late morning/early afternoon - beyond the commuting rush. In most cars, the first 2 seats up front face each other and you can stack some luggage between them. otherwise it's going to have to be a tight squeeze in your row or worst case, standing room only with you in the aisle if seats are scarce.
But don't worry. A ton of passengers get off at the "Newark Penn Station" stop which is a major hub in NJ to connecting rail lines and only 6 minutes away as the very next stop from the Newark airport. You'll easily grab seats then, and be able to spread out more comfortably for the rest of your trip in to NY Penn Station.
One youtube video to assist: "New Jersey Transit HD: Riding Train 7852 From Metropark To New York Penn Station (8 Car Arrow III)" - the first few seconds is quick look at the inside of the cars. (no need to watch the rest) You'll see how empty it can be.
If you have any questions, feel free to ask. We're all happy to help.