Greetings Jim:
At the end of the day it is whatever suits your fancy. I have seen both on models and the brass does look nice, the black iron more realistic. There were a lot of ships with rich captains or patrons that had at least some of the cannons in brass (one up on the other guy, eh). Plus I am sure you know that small guns like swivels were usually brass.
You could start by placing some brass cannons on the upper decks and look at them a while before making a final decision, or possibly leaving the quarterdeck guns brass and blackening the others.
Enjoy!
Bruce