Chef Mathieu Palombino is wearing a New Kids on the Block T shirt—and while it may be ironic, it's not inaccurate. Late last year Palombino, 31, opened Motorino in Brooklyn. His training was tony—Laurent Tourondel, David Bouley—but his latest recipe was rather primitive. Flour from Naples. Tomatoes from Naples. Cheese from Naples. And a massive, 850-degree, wood-burning oven built in Texas by, yes, a man from Naples. "My goal was to make traditional Neapolitan pizza," says Palombino. "The most authentic, the best." Local chowhounds quickly declared Motorino a success, but at least one group disagreed: Palombino's Italian-American neighbors. "They're like 60, 70, and they won't eat my pizza," he admits. "They prefer the place over there—the one with $2 slices." The new kid, it seems, was too old school for the block. And as impressive as his pies are, I get why.

Consider the New York slice. It's the city's most enduring gastronomical export: a cheap, cheese-slathered sliver of street life that has spread over the last century from the brick ovens of Little Italy to the farthest corners of the country, becoming both an icon of the Big Apple and the Platonic ideal of American pizza in the process. During the past six months, however, New York has been experiencing what The New York Times's Frank Bruni calls "a definite pizza moment"—a moment that threatens, I fear, to permanently alter what we think of when we think of New York pizza. Motivated by the new fad among foodies for upscale comfort cuisine, a slew of restaurateurs have opened pizzerias (Co., Tonda) serving Neapolitan-inspired pies enlivened with farm-fresh ingredients. Meanwhile, the premier purveyors of authentic N.Y.C. pizza are showing signs of strain. In January, Di Fara closed for weeks after aging pizzaiolo Dom DeMarco broke a kneecap. Totonno's burned down two months later. And the last of the storied slice slingers—Sal and Carmine's, Joe's—are few and far between. The result could be a coming shift in the city's balance of pizza power. "The New York slice is in danger," warns Sliceny.com editor Adam Kuban. "These highfalutin places are great, but they're a different thing. Losing the killer slice joints means we'll lose a way of life—walk in with $3 and eat your pizza on the street."

It's no help that what tourists typically take to be true New York pizza—the ubiquitous "Ray's Original" slice—is nowhere near as tasty as these new haute-Neapolitan pies. Recently I visited Kesté, where Roberto Caporuscio began making pizza in March. As U.S. delegate for the Associazone Pizzaiuoli Napoletani, Caporuscio is quick to note that throwback restaurants like his are simply returning New York pizza to its roots. In 1905 Neapolitan immigrant Gennaro Lombardi opened America's first pizzeria; by 1933, his employees had established the rest of the city's defining pizza joints. Over time, however, economic concerns intervened. The traditional 10-inch discs grew to 18 to satisfy American appetites; hard flour replaced soft, producing crust that kept for hours on a takeout counter. Soon came processed cheese, prefab sauce and fast-food franchising.

"The pizza from New York was not true pizza," Caporuscio says as he rotates a margherita pie over the flames of his Vesuvian-stone oven. "Naples is pizza." The pie that emerges a mere 80 seconds later is exquisite, with the acidity of crushed San Marzano tomatoes complementing the milky tang of fresh mozzarella di bufala atop an airy, chewy, slightly salty crust. Seeing me salivate, Caporuscio proudly adds that the waiting list for Kesté's pizza-making school is now seven months long.

I'm all for gentrified pies. But in New York, the slice is not only a meal—it's an experience. So I'm hoping a few of these next-generation pizzaioli dedicate themselves to preserving the pizza culture that Palombino's neighbors know and love. For proof that it can be done, visit Artichoke Basille's. One sweltering spring afternoon, a line of lunch-hour workers stretched out the door of the year-old storefront; every few seconds another famished nurse or carpenter emerged, lifting a slice folded inside a grease-soaked paper plate to his or her open mouth. Where the Motorino pie is delicate, Artichoke's is brash. A crisped slab of melted mozzarella, sloppy sauce and overabundant basil, it faithfully reflects the Staten Island upbringing of its beefy owners and pairs nicely with the shop's 32-ounce Buds. It is, in short, very New York.

At this point, Artichoke's crust is too stiff and its sauce too tame to compete with a Caporuscio creation. But it's exactly the sort of pie Di Fara was producing when it opened in 1964: a superlative local slice that could develop, with time and care, into a true classic. Sadly, recent events have shown that Dom DeMarco and his peers aren't immortal—"and once we lose Dom," says Kuban, "we'll lose his pizza." Joints like Artichoke—brazenly unfashionable, yet still obsessed with craft—are crucial to keeping the New York flame alive. My message to Gotham's gastronomes: save room for a slice.