Museo de Cultura Popular is a university-run museum focused on Costa Rican daily life in the late 19th and early 20th centuries. Its setting, a former residence associated with President Alfredo Gonzalez Flores, gives the displays a more intimate feel than a standard civic museum.
The museum is most useful if you want context for Heredia beyond the central park and churches. Expect household objects, customs, and local history rather than a large national collection.