The most straightforward presentation of shipfaring rules for a medieval setting is Columbia Game's Pilot Almanac for Harn. The downside it is out of print and considered a collectible. However I have been successful in calling or emailing Columbia Games direct and asking whether they will sell me a electronic copy or a photocopy of a out of print product. They are a small company and nice people.
The mechanics fit with Harnmaster but they are pretty a self-contained subsystem that easily can be used with another system. I used it with GURPS and OD&D myself. The mechanics are not that complicated and in my opinion are about as complex as classic Traveller rules for starship construction, crew and trading.
It is divided into several articles.
Pilots: Rules on the Vessel states, and mechanics for navigation and sailing .
Crew: information about Seamen, crewing a vessel, and mechanics for generating and hiring a crew.
Shipwright: information and mechanics for shipbuilding.
Maritime Trade: mechanics for handling maritime trade and cargoes.
Port Almanac and Maps: A list of port statistics to use with the sailing and trading mechanics along with four mini maps of Harn and surrounding lands.
There is also Worlds Apart a Travellesque RPG of maritime adventure and trading in the ancient Greece style (not Medieval) setting. It flaw is that is take the fantasy traveller trope too far in that instead of systems you have islands and so on. But there is a free version to check out to see if it suits your needs. And like classic Traveller it is straightforward to learn.