London and New York are not good comparisons to San Francisco. Although SF is a global city which is well interconnected with the rest of the world, it doesn't come close to London and NY, which are the greatest metropolises in the world in terms of ease of access to just about any human capital or other trade good in the world. They are also many times larger than SF, both in total population and population density, + public transport is a lot better. It is unreasonable to expect that they would be cheaper in proportion to their density.