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Not a lot closer. Tokyo to SFO on a jet is 9 hours. New York City to SFO is six and a half hours.

Don't forget about head and tailwinds. Tokyo to SFO is 9 hours, but SFO to Tokyo is 11 hours. NYC to SFO is 6.5 hours, but SFO to NYC is 5.5 hours.

More importantly though, you can get to a lot of Asia from SFO without changing a plane, that's not true of NYC.