Whadduya know, I'm in the middle of the same thing. I already applied to the Historic Preservation Commission to build a deck at my place (in the historic district) and it was a breeze.
Really nice people too (its the office of Construction Code Official where you apply for building permits that has been a royal pain in the ass). Anyway, just call the Historic Preservation Commission at 201-547-5010 and they will send you an information packet explaining the regulations in lay-man's terms along with specific information about different types of renovation and construction that might not apply to you (i.e., facades, signs etc.) AND a Certificate of No Effect/Certificate of Appropriateness.
Chances are if you're just building a deck and not altering the walls of your building, Certificate of No Effect is all you'll need to do (as was the case with me), and they will approve rather quickly, there's a $10 fee though. Certificate of Appropriateness, however, requires you to make 13 copies of the application and attend some monthly (sometimes twice monthly) meeting of the Commission. I don't know much about how that works because I didn't need to get that type of permit.
Now I'm in the middle of getting a building permit from the Office of Construction Code Official. I'd rather reserve my comments on them for another time, because I'm less than happy with them.
Good luck!