Hi!
You can take the dog and the kids to China Beach in China Camp State Park. Just take North San Pedro Road and stay on it until you see the beach (on the left). You can also get there by taking 2nd in San Rafael and staying on it a longggg time. From this direction the beach will be on the right. There are lots of rocks to throw, lots of beach glass. My kids are pre-teens to teens and have been having a good time there since they were babies. You'll need to keep the dog on leash, as the rangers are pretty attentive. I recommend bringing towels and change of clothes as the kids may get pretty sandy/wet/muddy.
Bowling is fun (in San Rafael). Cal-Skate in Rohnert Park is fun for roller skating. Also Scandia in Rohnert Park (mostly for the 13 year old though). You might also consider Chucky Cheese in Rohnert Park. Great for little kids, and the arcade games are fun even for older kids, at least for a while. You might look online to see if you can find coupons for them. I'd also check out your local pool. Swimming is great for all ages. Look for a movie both kids might enjoy.
I think there's a place on 4th in San Rafael where you can paint pottery. Also, a teenager will be briefly entertained by that cool park in San Anselmo with the big dinosaur.
Alright, that's all I can think of. Good luck!