Designer from SF
Combining your interest in lost places and small museums, I'd like to recommend the Lower East Side Tenement Museum, 97 Orchard Street, in the lower east side. This 1860's building is set up to reflect the various immigrant groups the settled in that area throughout the years. Each apartment is setup to reflect immigrants of different origins, and costumed actors recreate the day to day lives of these people. The ground floor is set up as a business from the past. There are walking tours of the neighborhood, as well as various events throughout the year.
For coffee shops, you should check out Devocion in Williamsburg. Beautiful interior that I'm sure you'd appreciate from the design perspective! Really good, strong coffee too. Hope that helps!