Take the BART subway in the International Terminal to downtown SF. Buy a $10.30 rt ticket in advance (required) and go to Powell St or Embarcadero station. A one-way trip takes exactly 30 minutes.

Mission/16th Street station gives a different view of SF but it has a reputation as a center of crime. Avoid it at night (same for Mission/24th).

Ferry Building near the Embarcadero is worth the trip.