X2 on Aquatic Park. Just be aware that the only thing you want to leave on shore is a towel and flip flops. Car key needs to go in your wetsuit everything else stays locked in your car, unless you have someone sitting on shore.
X2 on Sports Basement, basically a seriously dangerous place and if you have AAA, show your carxd for an additional 10% off.
I don't run in the city but if you feel adveturous head across the bridge to the Marin Headlands for a veritable buffet of trail running along the coast, its quite hilly but truly beautiful. There are a lot of fire roads as well as single trail that are fine with regular running shoes.