How about a small table to determine those fees and risk. For instance, you can dock in a safe location with local guards, services for loading and unloading cargo, etc. for 10gp per day. This can protect the boat from banditry and provide a bonus to moving cargo and resupplying.
On the other hand, you can go with the shady part of the docks with a lower fee of 2 or 5gp per day. If you do not leave enough of the crew aboard there is a risk of thievery. Of course, the crew will want to be off the ship to do what sailors like to do. Perhaps in the poor dock you will be approached for an unofficial "protection" fee as well.
Finally, you can anchor in the harbor at no cost, but the only way to move to the mainland or trade goods is via a small boat or skiff.
I'd even adjust the amounts randomly as larger harbors protected by by fleets and harbor defense require a greater tax to maintain. A dingy harbor without much traffic will be happy to accept a smaller fee or maybe even waive the fee based on good roleplay.
