The Bay Area has the highest concentration of Michelin stars in the country. The bars have great cocktails, decor and vibe. The SFMoma & DeYoung are first class museums as good as any city outside New York in the US.
The SFMoma & DeYoung are not first class museums. They have modern art. New York may beat San Francisco, but it is not particularly good.
The winning city, without any doubt, is Washington, D.C.
Also beating San Francisco:
Houston, TX
Huntsville, AL
Pearlington, MS
Kennedy Space Center, FL
Dayton, OH
Seattle, WA
San Diego, CA
Chantilly, VA
Ashland, NE
Unless you actually go to the same museum again and again, your own city doesn't matter. To see different things, you have to travel to different cities. The best city is thus one with lots of cheap direct flights to the cities with museums. That would likely be Denver, Dallas, Chicago, or Atlanta.
I'd also include Los Angeles (Getty and LACMA), Chicago (Art Institute), and Boston (MFA, beating SF by default because it doesn't even really compete in this category).
Getty and LACMA are not good. Los Angeles does however have good museums: the Battleship USS Iowa Museum, Fort MacArthur Museum, Mission San Fernando Rey de España, La Brea Tar Pits, and the California Science Center.
Chicago's Art Institute is not good. Chicago does however have a couple good museums: Museum of Science and Industry, Field Museum of Natural History,
Boston's MFA is not good. Boston does however have Fort Warren and the USS Constitution.
> The SFMoma & DeYoung are not first class museums. They have modern art.
These two statements aren't even related, and while the first is subjective, the second is misleading in regards DeYoung, which is not focussed on modern art.
They really are related. Modern art museums are something you endure to complete assignments for unpleasant humanities courses that are required for your degree. Most of the content is disgusting or boring.
I'd much prefer to see a Saturn V, mummy, XB-70, stegosaurus fossil, Space Shuttle, enigma machine, US constitution, SR-71, or moon rock.
The best museum in San Francisco is probably the cable car museum.
The DeYoung is mostly special exhibits, right? I've been to a couple that were pretty good but, in general, SF is pretty weak in terms of museums. (And I admit I just don't personally care for much of what's in SFMoma.) Though that's generally true of the West Coast with a few notable exceptions like the Getty.
I guess the permanent collection at the DeYoung didn't make much of an impression the last time I was there for a special exhibit. Never been to the Legion of Honor.
A great museum is likely to have events, speakers, special exhibits, and other new features that keep it fresh for residents. The Smithsonian system is very attractive in that regard; I can't vouch for the others.
I see you put Chantilly, VA on your list. The main museum of Chantilly is Udvar-Hazy, also part of the Smithsonian. Like the Smithsonian, it's free, though there's a parking fee (and it's in the middle of nowhere, so you do need a car.) It has many of the large aircraft that don't fit in the downtown Air and Space Museum, including a Space Shuttle, a Concorde, and an SR-71. Highly recommended.
I'll give you the Michelin star restaurants, but cheap or mid-range restaurants are disappointing (understandable given the astronomical cost to open and maintain a restaurant here), the bars and nightlife are similar to what you'll find in other cities, and museums in DC, Chicago, and LA blow SF out of the water.