I'd suggest checking three different places:

1) An address in the vicinity of the airport, like Millbrae (there's a cluster of rental offices around the Westin and the Marriott). A search for Millbrae on an OTA (like Expedia, Priceline, or, shameless plug, us) should also pick up other off-airport options in San Bruno and South San Francisco. All of those would be a very short cab ride from the airport...or you might even find a nearby hotel with an airport shuttle and use their shuttle. The San Bruno options would be an easy one-stop BART ride.

2) Check rates in downtown San Francisco. BART makes it pretty convenient to get from the airport downtown. There are lots of rental options within a few blocks of the Powell Street station. We get a lot of bookings for pick-ups on O'Farrell Street.

3) If she has the time and inclination, I'd also check downtown San Jose (and maybe the SJC airport, too). The rental companies consider SJC a different market, so rates are set independently there of demand in SFO. It's not too difficult to get from SFO to San Jose by CalTrain; there's a Hertz and an Enterprise only a few blocks from San Jose Diridon station, and both will pick you up from the station if you call them. SJC airport is a relatively painless shuttle bus ride away from the Santa Clara CalTrain station, and all the major brands are represented there.

She could also do the same in Oakland or at OAK airport, both of which are relatively easy to get to by BART.

It's all a balance of how much savings those options offer and how much inconvenience she's willing to endure to save whatever amount of money those options offer.

It can be worth checking, but it's impossible to answer in advance (without looking at the dates) whether it will help with any companies, much less all of them. If there's one thing we've learned about rental rates after helping north of a million customers, it's that there's no such thing as predicting rental rates.

As for specific companies...rental cars are largely a commodity, so you're fine to shop on price. That said, we sort of break companies down into three tiers:

Premium brands: Avis, Hertz, National
Value brands: Budget, Dollar, Thrifty, Alamo, Enterprise (and Sixt, to some extent)
Discount brands: Fox, Advantage, E-Z
...and then there's Payless.

There are also some considerations about which rental agencies handle out-of-town issues the best, which may come into play if she's planning on doing any road trips out of the area while she has the car. We covered that topic recently over in this post.