[Images via Big Picture]

I went in to the city this weekend, and for purposes of comparison (and being a scatterbrain), I went up via Jitney and came back via train. Below, a summary of my findings.

Cost: During peak hours a train ticket to Bridgehampton is $21 ($15 off-peak). A Jitney is always $29, and $51 roundtrip.
Time: My 9:16 train left Penn Station at 9:16 and arrived in Bridgehampton at 11:54. My Jitney was supposed to arrive at 4:45; pulled up at 5:07, and got to 40th and 3rd at 7:32.

My judge on Convenience, Comfort, Crowd, and Consensus to follow....

Convenience: Traveling aboard the LIRR necessitates dealing with Penn Station. The Jitney doesn't.
Amenities: The LIRR needs to fashion itself a snack bar, stat. The Jitney serves complimentary "party mix," chips, and water.
Comfort: It's no Excela, but the LIRR's seats are plenty cushy, and there's ample leg room. The Jitney is probably a little more cramped than the train, but the seats are plusher.
Crowd: Because I was going against the weekender wave, my fellow commuters on both train and bus seemed to be predominantly middle to lower-middle class. The train was also full of families with young children, and the sound of reggaeton blaring from uninserted headphones.
Consensus: Depends how often you're traveling, and how much you're willing to spend in the name of ease. Those with deeper pockets are better off with the Jitney (especially if they're willing to pay the extra $10 for Ambassador's class), while the frequent travelers and the patient are better off on the rails. That's my conclusion anyway; what's yours?