Which cities has the best science museums in the US?

I think it depends on which sciences you're talking about.

It's pretty hard to beat the Smithsonian Institute museums in Washington, D.C., esp. the National Air and Space Museum, but other major cities have multiple museums either within a campus setting or scattered around a larger area. Such as Los Angeles, Chicago, etc. Some museums have things you can't see anywhere else, like the space shuttle Endeavor and the La Brea Tar Pits both in Los Angeles, or the Manhattan Project exhibits at the Bradbury Science Museum in Los Alamos, NM. Some smaller cities have one museum considered world-class in a single discipline, i.e., the Monterey Bay Aquarium in California.

OMSI (Oregon Museum of Science and Industry) in Portland, OR is excellent.

The Exploratorium in San Francisco must be included in a "best science museum" category because of the huge number of live, in-person, experiments in action. I love this museum, but it is over-stimulating! https://www.exploratorium.edu/

The Museum of Science and Industry in the Hyde Park area of Chicago is a great museum.

Boston has a good science museum and so does Columbus, Ohio. The Cal Science Center in LA is also top notch. In fact, I think all those are better than the Smithsonian but that's just because the Smithsonian Air and Space only covers one topic, they cover multiple topics. FOr example, Cal Science has air and space but also other scientific endeavors. Si dies COSI in Colubmus. And of course, once you get into natural history, which I'd call science, that's a different story, The new Smithsonian rehaul of theirs made it better, I think NY's is probably better.

I imagine most or all of these are closed right now, though, and of course, I'd plan a visit around a trip for other reasons, but you can enjoy the science museums in all these cities named, I'd say.

Chicago for the Field Museum, the Museum of Science and Industry, the Shedd Aquarium, and the Adler Planetarium.