I wouldn t take 99. That freeway goes much farther east than you need, no matter what the traffic on 5 would be. 101 may be faster, but Im sure you ll be okay on 5. Sometimes, it backs up near the Altamont pass, one thing you can do is take 152 at los banos to gilroy and then up 101 to SF. I did that a few times and it seemed to take the same amount of time as taking 5 to the Altamont pass.Good luck!
It doesn t look like 99 goes near enough to San Francisco to be a viable option. Just grin and bear it, or try 101.