Mr. Suderow,

I strongly suspect that Lincoln just walked across the dock on the occasion that you mention.
Early in the war (1861), it was deemed desirable to build a spur from the Academy wharf to the Annapolis and Elk Ridge Railroad depot for the transport of troops and materiel.
I have the route (or actually the streets affected) outside the Academy grounds, but not within. The engineer company of the 13th NYSM was responsible for the track within the Academy. I have tried to locate their records, but without success.
As the Academy was given over to the War Dept for the duration of the war, it seems likely that military trains continued to operate on this extension, and Lincoln would have most likely used it.

Regards,

Ralph Osgood