I suggest looking along the edges of the neighborhoods you're interested in, or inside adjoining neighborhoods. Say you wanted to live in Park Slope. Better digs might be found downhill nearer to Fifth Avenue, north in Prospect Heights, or southeast in Windsor Terrace. You can also contact the Brooklyn Board of Realtors. The real estate brokerage world is pretty cutthroat in NYC, worsened by the fact that Brooklyn has no multiple listing of apartments.
Footwork is probably the best bet.
Visit the area and use your best judgment. In this city, whatever smells like a scam or a shady broker is generally just that. We have been considering Brooklyn. We are from Kansas City and Nashville and have never been to New York. I'm a recording industry professional and photographer and my wife is a make-up artist, so we have little money but a lot of ambition.