That is one old boxcar. It is actually derailed, rammed right over the bumper at the end of that track, which of course explains why it's been sitting there all these years. The bumper is crumpled under it, and if I recall right the truck is under it at a slight a angle. In fact, the entire car leans a bit to one side, where it's up against the concrete loading area.
My bet is that it will some day be scrapped in place.
Speaking of relics in the ares though, alcohol car W86 (?) is also nearby, parked along skillman av near the eastbound tunnel portals, and there's another old car, W17 if I recall right, at the end of the LIC passenger yard. No tracks lead toit, and I believe it is still used as an office or crew room of some sort.