I work in both the East Bay and Marin, and they are very different. All of these communities have real strengths, and weaknesses, of sorts. I would say that you might be better served to analyze what types of educational programs you feel like your children will be best served by, and look for the school that serves those specific needs, and then search for the house within the school system that you want. Start with the stats on the websites of the local boards of education for each city. I find that if I ask 10 different parents for an opinion, they will all give me a different answer based on their specific slant.
I also advise my clients, when they are moving to a new community they have not lived in before, to call local community groups, like neighborhood associations and parents groups, can be very helpful for identifying the strengths of individual education environments. These groups can be identifed through the school board, and through the poiice department community liason program. They usually have the names of the emergency preparedness groups, which plug you in to the specific neighborhood very quickly.
To the question of diversity, the East Bay definitely has a stronger Asian American presence, in Berkeley, Albany, Piedmont, Orinda, and Lafayette, as well as many other racial and cultural groups. I loved Mill Valley when I \lived there, but often felt hungry for greater diversity...in the East Bay, you have the entire world community at your fingertips. It's a rich and wonderful tapestry, with strong cultural groups combined with a high level of integration. Marin, overall, is considered tonier, and more prestigious, but also much more homogeneous. Marin will generally feel more small town, though it offers less commute options and is more of a car culture, where the East Bay has a more urban flavor, and offers a multitude of easy commute options. San Anselmo is an area you may want to explore, more than Mill Valley. SA is a very kid friendly area, with lots of young families having moved there for the schools. Piedmont is a city within a city. Orinda feels entirely upscale rural suburban. Big lots, lots of trees, few sidewalks, very kid oriented. Housing stock is \very pretty different in terms of age and architecture from community to community.
I would also want to hear what climate you hope to find, as the Bay area has a multitude of microclimates. Do you you like the cooler, occasional fog belts where things are more temperate, or do you want a hot, tomato growing climate?
So, it comes down to what specific educational programs you want to have access to, and what your personal aesthetic is for what will feel most like home. The agents you interview should be asking you many more questions, before offering advise. Good luck in your search!