Number one: GGP
The hands down the best bike path in SF is the:
Panhandle (no cars!!) →
Golden Gate Park (no cars!!) →
Ocean Beach → and back

The Wiggle is a short, bike-friendly, and least-hilly route connecting Market Street and the Panhandle.
Golden Gate Park is the pan. The Panhandle is the panhandle. The pan’s obviously too big for the panhandle
The Panhandle and most of Golden Gate Park has no cars. End of sentence. It’s safe, it’s quiet, not very crowded even during before/after work hours and not polluted. What more could you want?
If you’re lucky, you can also catch the infamous bison in Golden Gate Park
In 20-30 minutes, you can reach Ocean’s Beach
And you can enjoy some mangoes and elote.
Number two: The Presidio
The Presidio was established in 1776 by Spain to guard the bay from other European powers. It served an important military position during WWI and WWII
In 1996, Congress established the Presidio Trust to manage The Presidio.
It’s managed by the National Park Service and with the support of the Golden Gate National Parks Conservancy. On your bike ride you’ll see local herons. The bike paths are broad and mostly quiet and empty.
Number three: The Marina
Riding along the Marina is absolutely splendid.
My favorite place to visit is the wave organ. At the right hrs, you can sit in a nook and hear how the sound of the waves are captured to make organ-like sounds.
Enjoy biking in SF!