I'm a Brooklyn homebrewer, and have hosted Josh Bernstein's homebrew tour along with my brewing partner about six times. We aren't affiliated with the local homebrew clubs, but are active on the homebrewtalk forum and participate in area group grain buys.
Also -- everyone should be aware that Coney Island Lager is not brewed in NYC and really has nothing to do with the city, other than using the Coney Island name as a marketing tool.
Brooklyn Brewery (brewery - Brooklyn)
Park Slope Ale House (bar - Brooklyn)
Waterfront Ale House (bar - Brooklyn)
Henry Street Ale House (Bar - Brooklyn)
Heartland Brewery (brewpub - Manhattan)
The Gingerman (bar - Manhattan)
House of Brews (bar - Manhattan)
Also you should try Coney Island Lager, it's just a good beer
hope this helps...
Might I add Mission Dolores (bar - Brooklyn) Excellent rotation of domestic and international craft beers at excellent prices ($5 - $7).