I've done commutes on the LIRR using a Brompton. It's a fast, small fold and you can lay it on one side on the (relatively) newer overhead racks. If you're on a later stop and you won't get a seat anyway, the Brompton can be placed in front/side of you and will take up roughly the same amount of sq inches as a med sized roller luggage case.
My biggest issue was weight. It's not that 25lbs is heavy, but carrying it up and down stairs, through rush hour crowds, makes it seem much more cumbersome. You'll find that you'll unfold and roll it along whenever possible.
Also take into consideration any bag or backpack you'll carry with you.
I believe some NJ Transit trains (the ones I've taken from Newark's hub) have a special bike section. I've never used it, but it seems pretty nice.