There are a few apartment complexes in Novato. Can't claim that I know them all as I mostly do sales not rentals other than helping my clients rent out their investment properties.
However, I like the one next to 7th street and Grant Avenue (Marion Park); a couple along South Novato Blvd north of Delong and one on DeLong. - (Walnut Grove, Wyndover)/ There are also a few Rotary club sponsored Senior housing apartments.
There are also a few along Novato Creek.
However, you might be able to find quite a few condo / Townhome rentals by individual owners. That might be the alternatives.
Realtors also know a few properties on MLS (but to be honest, not as many as Craigslist) and a few good property management companies that might have the rentals.
Yes, Craigslist is a great place for rentals.