Newark Airport to Philadelphia on a Friday night?

One of the problems is that you will be in the middle of rush hour. Having gone to Newark Airport on NJ Transit (from NYC) in that time frame, I say with some authority that you might find yourself riding mostly illegally in the vestibule between cars, especially if you have luggage. Amtrak in business class is pretty nice, and you get free drinks which might be nice after a flight. The shared ride shuttles are kind of crazy - when I took one about 40 miles from Newark to home, it cost me $55 (in 2006). Dunno about the rentals, so I can't help you there.

Hmm, I agree that Newark Penn Station is unambiguous. It looks like Bolt Bus has added routes while I wasn't looking. Nevertheless, I'm glad you're going with Amtrak.

Amtrak. Make it easy on you. This will be an unpleasant leg of your trip no matter what you do.

http://ask.metafilter.com/208049/Newark-Airport-to-Philadelphia-on-a-Friday-night#2999062: "The Bolt Bus option seems ludicrous, frankly. To go from Airtrain -> NJTransit -> maybe PATH ->walking from WTC -> or Penn Station to Subway to then get on bolt to go to Philly. Wouldn't wish on my worst enemy." This isn't right. It'd be Airtrain -> NJTransit (direct to New York Penn Station) -> Exit Penn station at 7th Ave and 33rd and you're across the street from the spot where Bolt Bus leaves. No idea why anyone would take the PATH in this scenario at all, unless they mistakenly got on a NJ transit train to Hoboken instead of straight into NYC Penn.

As a veteran of the NYC to PHL via NJT and SEPTA, I will give you this advice if you choose to take them: Friday evening is the worst train trip of the week - it can be full of loud people and as you get later into the evening, some may be slightly inebriated. Those ear plugs/headphones you have with you for the flight are your friend. At the Newark Airport train station, I'm not sure if you can buy a ticket from the NJT ticket machine that will get you to Philly or not. If you can, do it. Otherwise you'll be buying a SEPTA ticket in Trenton from a person - SEPTA has no ticket vending machines. On your return trip to NYC, if you choose to use the SEPTA/NJT system, you CAN buy a ticket (two individual tickets in reality) from 30th St Station to NYC Penn Station. Do it all at once to avoid the hassle of having to get an additional ticket as you watch your train leaving the station. In Trenton, so far as I know, the SEPTA train runs every approx 40 minutes. This means that if you miss a train by a few minutes (known to happen), you're waiting a while. If you'd like to have someone to point a finger at, try SEPTA, they refuse to wait for the incoming NJT. They're charming like that. Best seats on the SEPTA train are the ones in the middle of the car - it is just one double seat on each side blocked off from the rest of the car. Grab it if you can. There's also more room for luggage. In terms of getting from one train to another, there will be other people doing this too, ask and follow them, they know what they're doing. Have a fun trip.

You'll have to research the particulars, but there's a bus called "http://www.boltbus.com/" that runs between Philadelphia's 30th St. Station and NYC's 6th Ave, about five or six blocks away from the WTC. Perhaps you can take the train from Newark to NYC, and the late bus from NYC to Philadelphia. They serve the commuter crowd, the buses are relatively clean and somewhat wi-fi'ed, and the fare is quite cheap.

Thanks for all the advice! I bought the Amtrak tickets.

As for getting to Philly from EWR, I would suggest taking the NJT/SEPTA combo as that's probably the most reliable and least expensive. Regarding Amtrak, my recollection is that as long as you have an Amtrak ticket, you can get on any later Amtrak train on that route. You might give Amtrak a call if you are strongly considering the Amtrak option. As for getting to NYC from Philly on Sunday, Blazecock Pilon's suggestion of BoltBus is spot on--there's also MegaBus that runs from 30th St Station in Philly to NYC. I've taken BoltBus many times and it is consistently cheap (<25$) and reliable (especially on a Sunday evening when there's little traffic).

Much of this depends on luggage and whence cometh you, i.e. how tired or jet-lagged you'll be. If you are lugging more than one suitcase or even a large unwieldy suitcase, I'd just take the $125.00 Amtrak. Remember you have to take Airtrain to the actual Amtrak station, so you already have one transfer no matter what. If the Amtrak is too pricey then perhaps take it to Trenton and then switch to SEPTA. You shouldn't have a problem getting on a later train. I take it to Philly & DC a lot and if I miss a train, hop on the next one, rarely a hassle except for the expensive Acela ones. The Bolt Bus option seems ludicrous, frankly. To go from Airtrain -> NJTransit -> maybe PATH ->walking from WTC -> or Penn Station to Subway to then get on bolt to go to Philly. Wouldn't wish on my worst enemy. I don't know about the shuttle rides, and I'd shy away from rental cars just for the hassle of parking in both NY and Philly. But really take the train, there are some times in life where it pays to spend a little extra dough. This might be one of those times.