What is the best place in New Jersey to leave a car and get into Manhattan?

It's no train, but - I used to take the NY Waterway Ferry from Weehawken into Manhattan.  24-hr parking on the Jersey side.  Lovely way to commute, though sometimes can be a bit bumpy. http://www.nywaterway.com/PortImperialWeehawkenTerminal.aspx

I spent almost two years working in New Jersey (near NYC) and I would suggest that the answer depends on where you are living. I have personal experience with the following train stations and I would recommend parking at them: Woodbridge Linden (although parking around to it the corner in front of the local VFW is a decent security option) Edison Union Summit Bridgewater Princeton Short Hills Hackensack I have parked my POV at all of these train stations, gone into NYC and I have returned w/ no damage to my vehicle and having had no problems as far as street crime. This doesn't mean that what didn't happen won't happen to you;I'm just relating my impressions based upon my personal experiences. I would suggest avoiding the following stations: Elizabeth - The security at this station is largely non-existent Rahway - Same as above Metropark (Too isolated at night) Trenton (Too isolated at night and getting your vehicle after it's been towed is a logistical nightmare) Harrison

Convenience may depend on where you're coming from.  For me, coming from upstate NY (ie the Northwest) the "Park and Ride" at the Secaucus stop on the NJ Railway has worked perfectly on many occasions--reasonable cost for parking, and 1-stop train ride leaving about every 5-10 minutes for Penn Station.

When I lived in NJ, I used to park in Harrison and take the PATH in. That might be the cheapest way into the city. If you're willing to walk about a half mile to the station, you can find free weekday parking.

Having done this several times… Drive to Hoboken. Park towards the bottom of Sinatra Blvd (it's right along the Hudson River) take the 5 minute walk to the PATH station and take the 5 minute train into Manhattan.

If you dont want a train ride (or just want the trip to be quicker) Jersey City or Hoboken - then you can take the path back (which runs like every 15-20 mins) rather then waiting on the actual train

I like the PATH station in Harrison. Parking isn't bad if you don't mind walking a few blocks and getting directly on the PATH is so convenient. Harrison is also pretty centrally located. But more than that I like parking at Port Imperial in West New York and taking the ferry to the city.

If you are coming from the south, Hamilton Station is a great choice to grab the NJT. Close to Princeton, but much more ample parking and highway access.