I just moved from SF to Manhattan. Apples to apples (insofar as it's possible), SF is more expensive.

Obviously I wasn't looking at single-family homes in Manhattan, but when it came to studios and 1BR apartments, the busy parts of SF (e.g., not the Sunset or Outer Richmond) are probably marginally more expensive than Manhattan.

If you want to get as close, lifestyle-wise, as possible, you're comparing Rincon Hill to Midtown, and Rincon Hill will be more expensive. Even if you expand the parameters out to the high-rises in western SOMA (towards crack-stab-town) SF will still edge out.

If you're comparing more residential-y areas, like, say, the Upper East Side to Hayes Valley or the Castro, SF will still win out, though you will probably get a tad more space in SF for your troubles.

It's hard to declare with great certainty who is the clear winner (or rather, loser), but SF is definitely neck and neck with Manhattan.

Or the whole Bay Area to NYC. This is comparing large tracts of semi-suburban areas (outer parts of Queens, Staten Island, etc.) to a <50 sq mile city. A closer comparison would have to include the Peninsula and East Bay at the very least, which are essentially SF's "boroughs".

The commute time by subway from Flushing, Queens to Lower Manhattan, for example, is about an hour. If you're willing to include that commute radius for NYC, the SF equivalent would also have a number of affordable places to live. For example, you can head 45-60 mins eastward on either the Dublin/Pleasanton or the Pittsburg/Bay Point BART lines. Or even closer, the going rate for a 2br single-family home in San Bruno (30 mins by Caltrain or BART) is around $2500.

I am not sure if there is any meaningful number of single-family homes in Manhattan. If you consider townhouses they are definitely more than $3500, even in Harlem.