Anywhere in Palo Alto, Menlo Park, Mountain View would be ideal. If you go closer to the 101 side, you have the Shoreline Baylands natural preserve w/ lots of Bike and Running paths. Anywhere in the mid-peninsula is great though.
Trust me, coming from LA (almost as bad as Manhattan), this is biking heaven here. Lots of protected lanes and cars are a lot more accustomed to seeing (the many) bike commuters.