Good schools are in many areas of Marin. Are you concentrating only on test scores to judge them?? What are the ages of your children??
For the person commuting to San Francisco, central San Rafael and south would be a smoother commute. However, as you go further south, the prices of homes increase. Therefore, you've asked a somewhat complicated question. What is your price range???
The Novato School District is quite diverse when you look at the different schools and programs at the elementary level. There are 3 middle schools and 2 high schools. In northern San Rafael, for elementary and middle school, there is the Dixie School District, which is quite popular. In central San Rafael, there are quite a few choices for elementary with Glenwood and Sun Valley generally having the best test scores. There is only one middle school, which is Davidson. There are 2 high schools run by the San Rafael School District, San Rafael High School and Terra Linda High School. The Ross Valley School District is good and services San Anselmo and Fairfax, which are west of San Rafael. However, that would add time to both commutes since you would be much further from the freeway. Corte Madera, Larkspur, Kentfield and Greenbrae all have good schools and are part of the Redwood High School District.
The bottom line is that it is more about your price range and the size of the house that you need. Once we have that figured out, we can give you better guidance.