On weekday mornings, 1 in 10 trains entering Pennsylvania Station arrived late, two-thirds by 10 minutes or more. At the peak of the rush, from 8:30 to 9:30 a.m., about 25 percent of New Jersey Transit trains entering Manhattan arrived late; about 2 in 5 of the late trains were tardy by at least 15 minutes. (The trains’ scheduled runs are a little more than an hour on average.)Even the New York Times misses on why trains are considered on time despite the fact that they are late to disembark passengers. Not only does NJ Transit consider trains late if the are more than 6 minutes over the scheduled time, but a train is considered to have arrived at terminals like Hoboken or Penn Station if they enter the attached rail yards. So, even if the train has to wait several minutes for a platform to become available, the train is technically on-time.
These are among the findings of an examination by The New York Times of the more than 685,000 trips in 2009 involving the region’s three major commuter railroads, using records requested by The Times that had not previously been made available to the public.
The review found that the official figures for on-time performance, often used as a promotional tool, contrasted sharply with the experience of tens of thousands of passengers who regularly ride the trains at peak hours. In fact, the most important trips for daily commuters, those that can make or break breakfast with a client or dinner with a spouse, experience far more delays than the statistics may let on.
Note too that one of the reasons for bottlenecks and delays on the NJ Transit lines serving NY Penn Station is the ancient 2-tunnel system feeding into Penn Station. It's at maximum capacity and the slightest problems with signals or a train breakdown cause a ripple effect causing delays for all trains through the tunnels in both directions. A delay of 5 minutes on 1 train will cause delays to 10-15 other trains in both directions.
That's a situation that will be somewhat rectified with the construction of the ARC tunnel, but that's not going to be available until 2017 at the earliest.