Looking ahead a little here but i'll be visiting New York in October. Would my beer options be better in Brooklyn or Manhattan? Or even somewhere else (relatively) central? Is there a "Visiting New York" thread like the ones for Portland, Seattle etc.?
There's a comprehensive list of bar, stores and breweries if you do a search. I'll say, this is a very challenging question. Manhattan has endless bars and great crawls, but it doesn't have a brewery like Other Half or Threes. And you didn't mention it, but the most breweries are in Queens and there are doable crawls, although the two I favor, Singlecut and Finback are a bit harder to reach. One thing to consider, you can easily do BK and Manhattan, so don't rule that out. There are a few threads discussing different crawls, but I have started at Other Half, hit Owl Farm, Mission Dolores, Threes and St. Gambrinus and then jumped on a train back to Manhattan and hit Fool's Gold and Proletariat. Everything I mentioned above should be on your agenda, by the way.
Agree with everything @ONovoMexicano said however the hipster crowd is minimal in Manhattan. Shoot me a message closer to when you come and I can provide suggestions, NYC is pretty good about updating beermenus so when its close you will know the best options that day.
Like OnovoMexicano said I would recommend Park Slope/Gowanus/Carrol Gardens and then you can jump on the F train and get to Fools Gold, Proletariat, One Mile House in 10-15 minutes.
My question would be - what do you want in your trip? Honestly, beer lists are so stupendous in New York right now, if you made any number of bars "home base" you'd be good to go - their tap lists turn over constantly and they often have many of the same "desirable" kegs as other bars (as breweries such as Hill Farmstead drop about the same time all around the city). You could keep track of beer events (brewyorknewyork.com is a good resource) if there is a special event or tap takeover you want to hit. The real question in New York is what else do you want to do - if you want to do Manhattan stuff, be in Manhattan, etc.
Rumor has it there's also other things to do in NYC in addition to hitting beer stop after beer stop.
If you do Manhattan, consider adding a museum or something cultural to your trip. I find art fascinating particularly after a few beers.
My vote is for Manhattan, for two reasons: (1) bars are closer together so it's easier to hop around if you see something you like on beermenus, and (2) Manhattan has a higher concentration of non-beer related activities - museums, landmarks, restaurants, etc. This is all high subjective though, so my best advice is to do some research on what exactly you're looking for. If you want to hit up breweries, you'll have to leave Manhattan. Other Half isn't the most comfortable brewery to hang out at, but the beer is pretty good, and Threes Brewing is close by and it's a great place to hang out and can have great food too, depending on who is visiting.