Brooklyn Bottle Shops/Bars?

Should probably be moved to the MA section, but Torst is at the top of that list. Other places I go to include Barcade (bar) and Breukelen Bier Merchants (store).

 

Breukelen Bier Merchants is pretty awesome.

http://breukelenbiermerchants.com/

One of my favorite spots to visit every time I go into Williamsburg/Brklyn. You can get some sick growlers or bottles there

 

Where in Brooklyn?

 

Arite, so you're slightly closer to Park Slope than Williamsburg (the two beer hubs of Brooklyn).
In your immediate area is going to be Downtown Bar and Grill, with a great beer selection and pretty good food too (though pricey).
For stores, you have American Beer Distributing Co nearby (check the dates on IPAs). Strong Place a few storefronts away has a great diverse beer selection and good food. A great under-the-radar beer bar/resto.

Park Slope is a bit further north, and there are tons of threads on good beer bars/stores nearby. Notably: Bierkraft for growlers (with a corner store a block away with much better prices on bottles to go).
Park Slope area bars to check out (listed by their distance from your area):
4th Ave Pub
Uncle Barrys
Mission Dolores
The Gate
Double Windsor
Washington Commons

As per Williamsburg recommendations, there are some good suggestions above, and other threads on this as well.
But don't forget Torst!