Yokohama History Museum looks beyond the port-city story to the deeper history of the area, from prehistoric settlements through medieval and early modern life. That makes it a useful corrective to the usual Yokohama focus on foreign trade and the waterfront.
The museum is especially worthwhile if you are already in northern Yokohama or visiting nearby archaeological sites and parks. It is quieter than the city's headline attractions, but it fills in the long local timeline behind the modern metropolis.