Another option is to park in South City close to 101 (on the street) and walk across 101 to Airtrain (about 10 mins). That runs 24 hours. My only question is how safe would it be to park, say,
here
On the other hand,
parking in Millbrae will mean a closer walk, but also a BART ride. BART's last Millbrae train leaves at 01:15 from SFO.