I haven't personally taken any training from either shop -- just stopped in for gear or fills. My brother did his OW/AOW from Atlantic Edge and seems happy and competent enough. I believe that Brass Anchor does their checkout locally, at Hyde's Quarry in Westminster, while Atlantic Edge travels to Dutch Springs, which means you're going to be paying for a nite or two in a hotel. Irrelevant of course if you elect to do a referral checkout someplace else altogether.
From our experience, Terry and Judy at Brass Anchor seem to have one of the better selections of gear in-stock which is why we ended up buying our wetsuits there -- I'd rather give my money to someone who actually has sizes to fit me in stock than having to order -- if I have to order and wait before even trying something on, I'll mail-order.
Interview the instructors and decide which one you like better. I don't know exactly how their programs differ (length of time, number of classes, pool sessions, etc) but pick the one that works for you.