What major US city (like top 50) would fare best?

Denver

Denver ?

Assuming just rain and no storm surge?

A city actually on the coast should handle it best since water doesnr have to drain far.

So maybe Miami

It's hard to say based on that, because that type of rain is even more abnormal in some areas than others.

Atlanta hit over 500 year flood levels in 2009 with 10-15 inches of rain.

without storm surge blocking flow to the Ocean, I would think a fair amount of major cities on the coast would be just fine

Salt Lake City. Remember several decades ago when they had a massive flood come down out of their mountains to the east, and they had constructed earthen levees to move the water through the city.

Denver, on the other hand, got wiped out when it was first founded by floods coming out of the mountains. Indians warned them, were ignored, and watched the settlers get wiped out. Same creek still floods, but some containments up in the mountains have reduced the problem.

Maybe Miami. But I don't believe any major city would do well with 50" of rain. Flat. Coastal. Mountains. Mud. That is 4 ft. of water that either stands or has to go somewhere.

Anchorage. It would just turn to ice.

While very few areas will be able to handle this type of rain and go unscathed, San Francisco itself would handle it better than most would expect. It's the west side of the surrounding counties of Sonoma, Marin, Santa Clara (San Jose last year) and San Mateo that would be under water. They are very prone to flooding and mudslides in years with above average rainfall (like last year). Petaluma (where I've lived for the past 30 years)-has some big time flooding when we get a storm that dumps 6-8 inches over the course of 2-3 days. 45-50 inches in 72 hours=toast.