After sleeping on this, I have think the port coffers should be filled using a Harbor Master tax/fee.
A percentage of all trade will slowly feed the coffers in each port. Now we all know some ports have more trade then others, but this is a good thing as it will potentially entice conflict over popular ports.
Each day MILLIONS of gold coin is traded between ports (crates and Gold Bars). These items need to have a tax/fee that a Harbor Master charges. Controlling nations will be able to set up their Harbor Master fee structure. I envision this much like the percentages on the Bank page. But this could further tie into diplomacy. Perhaps set up like this:
Nation Citizens = .01%
Allied Nations = .5%
Neutral Nations = .75%
Enemy Nations = 1%
****These percentages are just place holders. We need to know how much each port is taking in to come up with the best numbers that are good for the game****
These fees will be deposited into the Port Coffers and the controlling nation will be able to set how/where these monies are spent. Expanding Plantations, pay for Immigrants or future port expansions (FORTS and BLOCKADES).
Just spitting out ideas to keep the discussion flowing...