Some say Civil War spies buried the mysteriously missing pages of John Wilkes Booth's diary down there in a brass box. Others claim the tunnel holds weaponry from the notorious Smoky Hollow gang, bootlegging treasures, clues of 19th century espionage, and plenty more.
In 1861, Walt Whitman wrote a column in the Brooklyn Standard where he describes "the old tunnel, that used to lie there underground, a passage of Acheron like solemnity and darkness, now all closed up and filled up, and soon to be utterly forgotten, with all its reminiscences..."
The tunnel was rediscovered in 1981 by engineering student-turned-Brooklyn's own Indiana Jones, Bob Diamond. Diamond spent years in search of the tunnel and its supposed secrets. After scouring ancient engineering documents, obtaining city permissions, and crawling on his belly through 100ft of Brooklyn soot he was finally rewarded when he was poked through a hastily constructed brick and cobble wall and felt a blast of cold air rushing out from the 120 year old cave.
Currently there is a documentary is in the works exploring his great find and this amazing story. This trailer is pretty good insight to the story...
The tunnel was originally commissioned by Cornelius Vanderbilt's LIRR in 1844 when the nuisance of train-related pedestrian bloodshed was gumming up his all important train schedules. A small army of Irish workers did the digging, known later as sandhogs, using the cut and cover method and in truth, it became New York's very first subway.
By the 1850's the tunnels usefulness was waning so a contractor named Electus Lichtfield was hired to fill in the tunnel once and for all, but these being the glory days of New York construction corruption, graft and all around corner-cutting, Lichtfield does not such thing. Instead, in the interest of making a grand ole' profit, he walls in the tunnel on both ends, covers up the other entrances with cartloads of brick and dirt, and get some his "friends" at City Hall to confirm that the tunnel was gone forever...Bob Diamond's incredible story of rediscovering the tunnel eventually uncovers Lichtfield's scam but his great con turned out to leave something of a legacy for New Yorkers in search of a little intrigue. Still, there are two areas of the tunnel that have not been opened up and Bob Diamond believes that Booth's diary and other lurid artifacts may still be entombed there. Diamond is now the official curator of this great piece of NYC archeology and occasionally runs tours of the defunct tunnel that Whitman called "dark as the grave, cold, damp, and silent."
There is a great collection of in-depth tunnel-related articles here: http://www.brooklynrail.net/proj_aatunnel.html
You can also read the story at Curious Expeditions: http://curiousexpeditions.org/?cat=35