Unseen city

Descend through a manhole to a 166-year-old tunnel, glimpse rare-bird habitats in the Bronx, or get a taste of bygone Brooklyn. These off-the-beaten-track tours reveal secret worlds that would surprise many New Yorkers.

Photograph: Lee Magill

New York is full of unmissable landmarks, but scratch the surface of this multilayered, multifarious metropolis and you'll uncover strange relics, hidden subcultures and wildlife strongholds that let you see it from a whole new perspective. Some of the most fascinating discoveries can only be accessed through a knowledgeable guide. So forget any preconceptions you might have about group tours; chances are locals will outnumber out-of-towners on these unique urban expeditions.

Slip below street level

Far more than an introduction to America's oldest subterranean transit tunnel, Robert Diamond's tour through the half-mile-long Atlantic Avenue Tunnel is a (multi-chaptered) story you'll never forget. Built by hand for the Long Island Rail Road by Irish immigrants in 1844, in part to stop the widespread deaths caused by brakeless trains through downtown Brooklyn's city streets, the massive tunnel had a brief working life. It fell out of use in the late 1850s, and after local businessman E.B. Litchfield was hired to fill in the subterranean passageway in 1861, it was widely assumed it had vanished forever—until Diamond, a 19-year-old grad student in 1979, heard mention of it on the radio. In an item on a book about the assassination of President Lincoln, it was mentioned as the possible location of killer John Wilkes Booth's diary. The idea that the tunnel might still exist quickly became Diamond's Holy Grail, and against all odds—and after countless conversations with scholars, historians and city planners, all of whom told him he was wasting his time—he wound up in the Brooklyn borough planner's office, convinced employees to open a locked chest and found the tunnel plans within. Its location revealed, he set about gaining entry.

This is but one of the fascinating stories Diamond tells underground, after you've descended, one by one, through a manhole in the middle of busy Atlantic Avenue, down a steep set of wooden stairs and into the tunnel, which feels—and smells—like a vast, exitless cave. Other tales involve bootleggers, hidden Mafia bodies and more exploits of the swindling Litchfield. In the near-darkness, history is made, forgotten and conjured before your very eyes.

Atlantic Avenue Tunnel Tours cost $15 and are usually offered twice a month (1-718 941 3160, www.brooklynrail.net).

Infiltrate urban wildlife habitats

New York is rarely thought of as a lush, dynamic eco-system, let alone as one of the most important nesting grounds for endangered bird species in North America. But it is both, and the best way to see for yourself is aboard the Aubudon Society's guided water-taxi tour up the East River to the Brother islands, between the Bronx and Rikers Island. South Brother Island, which has been uninhabited since 1909 and became city property only in 2007, is home to about 200 pairs of great egrets, 200 pairs of snowy egrets and 400 pairs of black-crowned night herons, along with an assortment of ibises, gulls and cormorants, according to Audubon NYC's executive director, Glenn Phillips. Led by an Audubon naturalist, the excursion takes you through the rich natural history of New York City's double life as an estuary, passing U Thant Island, behind the U.N.; residential Roosevelt Island; and Mill Rock Island—another uninhabited, thriving breeding ground for migratory birds—along the way. The best is saved for last: the tour is exquisitely timed to arrive at South Brother Island just as the egrets are returning from a day of foraging in the New Jersey Meadowlands and the night herons are departing to do the same nocturnally—one evening rush hour that's truly astonishing.

Audubon EcoCruises cost $35 ($25 reductions), departing from South Street Seaport's Pier 17 at 7pm on Sundays from June 6 through August 15 (1-212 742 1969, www.nywatertaxi.com).

Savor Brooklyn's brewing legacy

Urban Oyster, a small tour company hoping to keep NYC neighborhoods from going the way of its oysters (plentiful and inexpensive in the 19th century, they were polluted to inedibility by 1927), is keeping the history of Brooklyn's breweries alive. By 1976 not one of the breweries—which numbered 48 in 1907, producing a remarkable 77.5 million gallons a year—was left. More than a century later, Brooklyn is once again booming with culinary start-ups, from chocolatiers to cheesemakers, coffee roasters and, yes, brewers. An eclectic ramble through Williamsburg and East Williamsburg, the tour starts at Brooklyn Brewery, the first of the borough's three currently operating microbreweries to open (in 1996). You'll take a private tour of the operations, then sit down for a tasting of all the beers in house that day, from its standard-issue lager, brown ale and Weisse to seasonal specials like Post Road Pumpkin Ale (out in August) and Brewmaster's Reserves, the small-batch concoctions of brewmaster Garrett Oliver.

With a slight buzz on, you then hop into a van and head east to Brewer's Row, the former epicenter of beer making, to ogle former breweries, learn why they flourished, then stop at Danny's Pizza for ultra-fresh slices. Afterward, you'll end up in one of the neighborhood's most charming spots, Huckleberry Bar, to sample more local brews along with house-made small plates.

Brewed in Brooklyn Tours cost $49, offered on weekends from March through December (1-347 599 1842, www.urbanoyster.com).