Obviously you have several factors in play, and available land is one of them. But both SF and Manhattan would be cheaper than they now are if they had Chicago's more liberal attitude towards development, construction, and rent controls. Not as cheap as Chicago in the limiting case, but still cheaper. Indeed, even if SF had only New York's somewhat more draconian attitude towards development, it would be a lot cheaper than it is now. Rents in SF are comparable to Manhattan even though Manhattan has half the land area and twice the population.