I found the Peekskill Valley Railroad on Joseph R. Bien's 1893 Cortlandt town map. It's much more detailed than the 1881 Bromley. If it's to be believed, then the bridge in the center of this map:
http://mapper.acme.com/?ll=41.31849,-73.91632&z=19&t=S
is in the exact same location as the railroad bridge. Southwest, it goes through the landfill, is probably underneath the modern road, and any remains of the trestle crossing Peeks Kill is probably underneath the fill they dumped into the wetland. Northeast of that you have houses built up to the creek, so if there remains any trace, it's just a bit of flatness here and there. Then you get up to the Cortlandt Lake dam, and after that, you're off the 1893 map.