On top of the world: Aerial photographer Alex MacLean uncovers the secrets of New York's skyline

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Is it a bird? Is it a plane? Well, yes. It is a plane, perched at the end of a bright green Astroturf landing strip up on the roof of 77 Water Street, in the heart of Manhattan's financial district. When the William Kaufman Organisation built the 26-storey tower in 1970, its owner requested something more interesting than air-conditioning units to top it off, to amuse his taller neighbours as they looked down on his rooftop from their skyscrapers. And so a rusty replica of a 1916 British Sopwith Camel biplane was lowered into place by a crane and has remained there ever since.

You'd never know it was there, of course, unless you climbed up high. Or unless you chartered a helicopter and hovered dangerously close to the tops of New York's buildings like a pesky giant bluebottle. That is exactly what Alex MacLean spent the best part of two years doing, armed with his camera. The surprising, smile-inducing results can be seen in Up on the Roof, a new book of photographs dedicated to the city's secret rooftop spaces.

Just when you think you've seen every breathtaking view New York has to offer comes a bird's eye view of a Williamsburg apartment block with – can it be? – a miniature putting green on the roof. Or an aerial shot of an unlovely office building in Brooklyn Grange, Queens, topped off with a one-acre organic farm, planted neatly with row upon row of tomatoes, peppers and aubergines.

There is a whole other city up here, high above the exhaust fumes and exhausted pavement-pounders, from 'sceney' swimming pools in SoHo to hushed, lush gardens on the Upper East Side. Up on what MacLean calls the "fifth façade", there are beehives and basketball courts, cocktail bars and herbaceous borders, adventure playgrounds and one-of-a-kind artworks – all of them hidden except to those who are in the know or who own an apartment on the 40th floor or above. Most tourists at Moma probably have no idea that its roof, inaccessible to visitors, features a black, white and turquoise design, like a giant Picasso in gravel: it's a visual treat reserved for the eyes of its high-rise neighbours only.

MacLean has captured people, too, crowding the rooftop pools and tastefully-decked bars of Manhattan like camels at a watering hole in the desert. Best of all are the moments when New Yorkers are caught unawares – a rare occurrence in the city that never sleeps. A pair of pasty legs pokes out from a sun-lounger tucked behind an ornamental bush, blissfully undisturbed by the yellow cabs zooming a few floors below. f A smartly-dressed crowd, all pale suits and pashminas, toast a bride and groom atop a brownstone in West Village. On top of the Standard Hotel in the Meatpacking District, crowds of guests stand outside a high-altitude café selling crêpes.

"There's a lot of chance involved in getting a shot. I would liken it a bit to fishing. You have to spend quite a bit of time at it but at the same time you have to plan where the fish might be and go after them," says MacLean.

There's also quite a lot of courage involved. MacLean shoots his remarkable pictures through the window of his lightweight, composite plane, banking it steeply and tilting his camera perilously to get the perfect straight-down angle. "I was terrified when I started. The first 20 hours, all I could think was, 'What happens if I fall out?'," he says. "I was always a very nervous flyer so learning to fly was a kind of counter-phobic reaction." Happily, he has never fallen out and has only dropped his camera – or rather his zoom lens – once, while shooting over the Ohio River in Cincinnati. "It fell right into the slipstream and the air just ripped it out of my hand. It was like a war movie when you see the bomb dropping. We were over a housing development and all I could think about was the lens going through someone's roof and landing in front of people as they watched television. In the end, it landed in some woods. I was so relieved."

MacLean has been documenting America from the skies for over three decades. He learnt to fly while studying architecture at Harvard in the Seventies and started out providing aerial images and site analysis for architects, landscape designers and environmentalists. Along the way, he started to take his own pictures, of natural features and agricultural patterns, and published his first book A Look at the Land in 1993. Some 6,000 flying hours later, he has published nine more books of aerial photography, f all focusing on the interplay between natural and man-made landscapes, whether stadiums and theme parks in The Playbook or man's detrimental effect on the environment in Over: The American Landscape at the Tipping Point.

"When I'm shooting something," he says, "I'm always looking out of the corner of my eye at something else." He was photographing the construction of Brooklyn Bridge Park for a commercial commission when he spotted a strange, castle-like structure on top of a building in Tudor City and zoomed over to take a closer look. On the way, he discovered there was a lot more to the New York skyline than the ornate Art Deco "party hats" of its most famous skyscrapers. So he hired a helicopter, which allowed him to fly at a much lower altitude than in a plane, and set off to chronicle the burgeoning rooftop scene.

It is, says MacLean, a relatively recent development. Projects like the High Line, the disused railway track reclaimed as an elevated walkway in Chelsea, have opened New Yorkers' eyes to the aesthetic and leisure possibilities of their previously unloved flat roofs. The eco-friendly 'roofscaping' initiatives of Mayor Bloomberg, meanwhile, have transformed the tops of buildings into a utopian model of green-city living for the future. Where once were ugly fans, ducts and pipes, there are now solar panels, 'green' roofs (covered in plants to retain water, and both insulate and cool buildings), 'white' roofs, painted to reflect the sun, kitchen gardens and urban beehives. "Instead of being a pessimistic look at the American landscape, it's really an optimistic look at the opportunities of the city," says MacLean. "The hope is that people become aware of the potential that may be right over their heads – extra space to catch some fresh air and make the city just that bit more habitable."

The photographs are also undeniably elegiac, with the city's highest rooftops, those of the Twin Towers, striking by their absence. Their replacement, Two World Trade Centre, will be the tallest building in America (at 1,270ft), when it is finally topped off in 2014. When that day comes, MacLean will surely be hovering nearby, ready to capture the secrets of its diamond-shaped roof from his cockpit.

'Up on the Roof: New York's Hidden Skyline Spaces', by Alex MacLean is published by Princeton Architectural Press in May