While the total travel time may be close going via JFK requires catching the 6am SFO-JFK flight, which makes for a long travel day coming from the west coast, lie flat or not.

ORD let's you grab the 8am SFO-ORD, not that much better but 2 hours is still 2 hours.

Personal preference but I'd probably go ORD; Shorter domestic connecting leg, slightly longer overnight TATL segment, and 2 extra hours of sleep the night before.