Hmm...
(1) May be a transponder for CBTC (Communications Based Train Control), depending on what line you took the photo on.
(2) The lunar-white signal target is found on timer signals (they clear after a specified time interval as a train approaches as a speed-control mechanism)
(3) Don't know what the object on the third-rail cover is, but it's no doubt painted yellow to make it noticable to track workers. I want to call the "pipe" a gauge rod of some sort, but I will hold off on that.
(4) The handle is a "stop arm". It's raised whenever its associated signal is red. Run past it and it will kick out a valve sticking out from the trucks, triggering the emergency brakes.
(5) Could be signal or power infrastructure
(6) Don't know about the "high" drain cover, but the double rail is a guard rail, placed next to the inner rail on a curve to bear the outward forces of train wheels passing through it, so the outer wheel's flanges aren't biting into the side of the railhead.
(7) Those flatcars are typically seen on work trains that attend to track-replacement projects where the concrete roadbed is being demolished. The yellow subway car is called a "rider" car, carrying work crews and equipment to/from the jobsite.
(8) See #4
(9) Probably groundwater. Manhattan did have a number of springs and streams before it was all built over.
---PCJ (answered to the best of my knowledge, Others may have more detailed info)
