Well I'm not quite sure just what the problem is, however I do have to wonder if it's catenary related. My reasoning is thus, whatever the problem is it is affecting the LIRR. The LIRR does not depend on catenary for power; they instead use third rail technology. Yet I noticed during a visit to my favorite Queens supermarket, located right next to the LIRR - Amtrak split, that the LIRR had inbound trains stacked up 5 trains deep.
Unless the catenary had been ripped off the roof of the tunnel, they should be able to reverse the normal flow of the inbound tunnels to keep trains moving. Even if the catenary had been pulled down, I still don't think that the number of inbound trains at 7:00 PM is that high such that it would create the huge backup that I saw. So I for one think that something else is afoot here.
On a separate note, northbound Acela Express #2172 the 7:00 PM departure, was by and largely on time. It passed me at my vantage point at 7:14, which probably only puts it down by about 4 or 5 minutes.