It looks like treating facilities available at settlements as magic items might actually work quite nicely. And if you are overly concerned about the cavalier discussion of +5 magic items, just remember that it is a lot easier to get a 11th level settlement than it is to get a 11th level character (the minimum to have a chance of producing a +5 magic item).
Ports, Harbours, and Wharves (Trade by Water)
A settlement located on a navigable waterway (such as a river, lake, or coast) may develop trade via that waterway.
Waterway Access (+0 Water Trade)The settlement has access to a navigable waterway but has not done anything to substantially develop this access to make trade easier or simpler. Local water merchants may stop and peddle their wares, but most will have little incentive to, because of the difficulty of access.
If a settlement located on such a waterway does not have this level of access, then there is some obstacle to easy access to the water. Perhaps the settlement is located on top of a cliff, the shoreline is too treacherous, or the waterway is excessively tidal. Investment can overcome these obstacles, but the amount required is quite substantial and would act as a Drain on the settlement, rather than a Boon.
The settlement has constructed a dock to make it easy for the river trade to access the settlement. Local water merchants and the local passenger trade may stop at the dock, but most traffic will still be passing it by. Some small boat fishermen may make use of the waterway, with the boats generally pulled ashore at night.
Dock (+1 Water Trade)
Wharf (+2 Water Trade)The settlement has developed the dock into a more substantial wharf in order to take full advantage of the local water trade. This will often include a trading post and warehouse (or possibly even a regular) market, through which local trade can pass to the water trade. Small boat fishermen will help supply the village with food, but there is no safe harbour for their boats. Larger boats may dock at a wharf.
Harbour (+3 Water Trade)The settlement has a harbour that is reasonably protected from the elements typically experienced by the settlement. This means that the settlement is capable of supporting a permanent maritime presence, usually in the form of a heavy fishing presence and base for the local water trade. There will be a dedicated fish market and a source of supplies for mariners, although many of the supplies are likely to be imported (unless hemp is a major crop a ropewalk is unlikely). A Harbour may or may not be able to handle ships. A harbour may feature a boatyard (a facility for building boats and small ships), and if so, their is a possibility of a Shipwright in residence (in which case "Boats" will be a notable trade item).
Most harbours are natural occurrences which are then developed by the settlement. They can vary heavily. For example, a long sandy beach may make a good "harbour" for a galley fleet - during the stormy months the fleet can be drawn up on the beach, careened, and repaired, to be refloated once the storm season has passed. Most coastal settlements are well sited to take advantage of any natural harbours, given the importance of the water trade for bulk haulage and the production of food, even if the facilities for trade are not as yet available. Such sites are often favoured by local smugglers (see Port, below), because they can carry on their activity [mostly] unobserved, although such "trade" often has to use lighters and small boats to make it ashore. For example a Manor with Waterway Access might have a secluded cove suitable for bringing small boats ashore, as well as convenient cellars to store the goods out of sight - at least until the old Copper Mine starts producing... That said, many settlements along a river won't have the facilities (or need) to establish a harbour, and any coastal settlement without initial Waterway Access will not be able to without extremely expensive (magical) investment to create a usable artificial harbour.
This is the minimum requirement for the establishment of a permanent naval presence (Water Military) at the settlement, although, as always, the navy may "recruit" fishermen and sailors from lesser facilities. However most settlements will not have a permanent naval presence, which is why it is considered an extra expense.
Port (+4 Water Trade)The difference between a Port and a Harbour is that bringing foreign goods into a Harbour (or lesser facility) is technically referred to as "smuggling" - an activity that is frowned upon by the excisemen and exchequer (a Port is almost always a Royal possession). The facilities at a Port are capable of handling international water trade as well as the local water trade, with many wharves and warehouses, as well as all the support facilities required to support maritime endeavours, including the guaranteed presence of Shipwrights as well as boatyards and shipyards.
Ports always connect with the national land trade (increase the Road Trade bonus by +1). There is likely to be a permanent Naval presence at a port (increase the Navy bonus by +1 if applicable).
Free Port (+5 Water Trade)A Free Port is one where much of the port facility has been granted a degree of extraterritoriality - at least as far as customs and excise are concerned. This means that foreign goods can be legally brought into the port area without attracting an import tariff, provided that they remain within the port area and it's bonded warehouses. This make a free port an ideal transhipment points for goods, which increases the amount of goods flowing through the port, and thus the wealth of the port (and tax paid to the sovereign). The extraterritorial portions of the port are usually walled, gated and actively guarded to discourage smuggling. The standard tariffs and excise are applied to goods actually brought past this wall (in either direction). Additionally the facilities to support this trade bring in large amounts of wealth, making it very profitable for all concerned.
Free Ports always connect with the national land trade (increase the Road Trade bonus by +1). There is likely to be a permanent Naval presence at a port (increase the Navy bonus by +2 if applicable).
NotesRemember that the Road Trade bonus is likely to be much less than the Water Trade bonus, because roads are not the best methods of shipping goods in the historical periods covered by these rules. This is why the parasitic Road Trade bonus from a Port is limited.
[If you are curious about why I've been very unsuccessful at writing up my house rules, this entire post exists as a six line/14 word table in my notes.]