What Woody Allen has done for Manhattan over four decades, brothers Ben and Casey Affleck do for their beloved Beantown in the new film “Gone Baby Gone.”

This is a classic Yankees vs. Red Sox showdown, cinematically speaking. If Allen is Joe D, then the Afflecks are Yaz.

“Gone Baby Gone,” the Dennis Lehane-based novel that delves into the case of a missing child but, by examining our own humanity, digs much deeper than that, is more than an exceptionally executed mystery. It’s a look inside Boston from a couple of brothers who grew up there and use that expertise to make one of the most pleasant surprises of the year.

And, oh yeah, the moral quandary at the end is a whopper, worthy of hours of post-movie/late-night dinner discussion.

Ben Affleck’s directorial debut is a full-scale triumph, one that quickly makes filmgoers realize that the actor who has often been mocked for his choices of acting projects — “Daredevil,” “Reindeer Games” and, of course, “Gigli” — has found his real strength behind the camera.

Affleck lets us see his Boston via the gritty blue-collar towns of Dorchester, Roxbury, Chelsea and Everett. Several of the characters in the film are actual hardscrabbled townsfolk, men and women who’ve been through hard times. It comes across in their scars, in the way they walk, in what they drink at the local dive bar, and, of course, in that distinctive northeastern accent.

Case in point: Dottie, the best friend of Helene, the mother whose daughter was snatched. She talks back to the cop with a gutter mouth and doesn’t take an inch of guff.

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Dottie is played by Jill Quigg, a woman who had never acted a day in her life. She wandered on to the set one day just when Affleck happened to be looking for a woman with an authentic Boston background. Soon, she found herself in the movie.

As for Helene, this feisty mom feels like she was born on those streets as well, which is a tribute to actress and two-time Tony nominee Amy Ryan. While Helene is a drug abuser and far from parent of the year, to cast aspersions on her as an unfit mother would be wrong.

“I think one of the things about the movie is that it shows people for who they are without really judging them,” Ryan said. “They might have broken wallets or even broken souls, but there’s a humanity to all these characters.”

For all the great performances here — Ryan, Ed Harris, Morgan Freeman, Michelle Monaghan — Casey Affleck’s role as a neighborhood investigator trying to uncover the truth about the missing girl is the most astonishing. Not because he’s so good, which he is, but rather because we’re left asking ourselves, “Where has he been all these years?”

At 32 years old, Casey has a brilliant career ahead of him. He also received raves for his turn in “The Assassination of Jesse James By the Coward Robert Ford.” If he’s been in older brother Ben’s shadow before now, it’s time to let that light coming pouring through.

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