There's stuff on this in the past threads somewhere, but I don't honestly know how to find a link to that.
It's a 2 or 3 of years since I've been, but I've posted photos over time and a Brooklyn guy, Tim, commented in February, regarding A-1 Records being open:
It still is as of Feb 4 '13, as are Academy's three stores.
Here's Tim's link:
https://www.flickr.com/photos/13873181@N06/
Academy Records Brooklyn store is in Wiilamsburg, well worth a shot, lots of cheap 7" and plenty of albums. Their other store at the top end of East Village over towards Avenue A is smaller but also worth dropping in on, and not far from A-1.
I put them on a Google maps while ago, so a fair few of these have closed (sadly including Big City, good place for Soul):
https://maps.google.co.uk/maps/ms?msid=203611530700193463245.000482b970fd77323e5a8&msa=0