Google Maps does a generally good job of public transport in the bay area.

In addition to the options mentioned above, you could also catch Caltrain to San Jose Diridon station, and then catch the VTA light rail, followed by a short-ish walk. The only disadvantage of this over the VTA 10 bus from Santa Clara is that VTA 10 is free, whilst the light rail isn't.

Keep in mind that any Caltrain trains at this time of night will be "local" train, aka all stops which means it'll take over an hour to get from Millbrae to Santa Clara, and the trains only run (at most) once per hour so if you miss one the whole trip could take up to 2 hours or more.

The good news is that at that time of night, BART goes directly from SFO to Millbrae, without having to change in San Bruno.

(FWIW, BART prices went up recently - SFO to Millbrae is now $4.25)