BART: comfortable, fast, limited locations in the city but reasonably good coverage of East Bay and it will get you to the airports (SFO and Oakland). Price varies based on number of stops but roughly $4 to $8 is a reasonable set of bounds.
Light rail: comfortable, fast, moderately good coverage of the city. Price is fixed ($2 / ride)
Bus: Uncomfortable, slow, but excellent coverage of the city. Price is fixed ($2 / ride)