I live and work in Marin. I'll post up Marin recommendations first, then Sonoma.
Food and drink: If you like beer and brewpubs, I suggest giving Marin Brewing Company a try, they are located in Larkspur Landing. They have a great IPA and outdoor seating. They also have a sister brewery in Novato, Moylans. Food is only so so, but the beer is great. I'd also give Iron Springs Brewery in Fairfax a shot. A bit out of the way but it is on Sir Francis Drake if you are heading toward the coast. There is also Lagunitas brewery in Petaluma, but I don't personally care for their beer. Pelican Inn at Muir Beach is a neat place to have a drink.
Breakfast: I can recommend Half Day Cafe in Kentfield and the Dipsea Cafe in Mill Valley. Also consider Theresa and Johnny's on fourth street in San Rafael (cash only) and the Crepevine, which is a little further up fourth street. There is also Lighthouse Cafe in Sausalito. All of these can be busy on weekends.
For lunch you have lots of options. I would definitely check out Sol Food in downtown San Rafael, they have the best Puerto Rican food in the area. Scomas in Sausalito had good seafood, can be pricy, but you can enjoy a meal right on the water. I also like Gott's in Greenbrae (The best is the St. Helena location, the original).
For lunch or dinner, I highly recommend the Station House Cafe in Pt. Reyes Station. Food is fantastic, and the popovers are outstanding, but popovers served only after 4. Pt. Reyes Station is a fun little town on Highway 1 that you should definitely check out. Further up Hwy 1 try Tomales Bay Oyster Company. Great oysters, shitty parking. Pizza here is a wash, and I'll skip recommending Mexican since your options are better further south.
These are all places that I eat at regularly.
Places to avoid: Marin/San Rafael Joes. Stinson Beach--shitty parking, but might be OK for an AirBnB.
Getting around Marin: Drivers here don't suck as bad as the drivers in the East Bay/South Bay, but can be very clueless. Hwy 101 north is crowded during the afternoon commute and comes to a standstill at the Novato narrows. Getting to the coast from 101 easy. Most people go through Mill Valley by taking Panoramic, if you were going to hit Muir Woods then drive to the top of Mt. Tam and head over to the coast that route is OK, but crowded on weekends. An easier route is taking Sir Francis Drake through Fairfax and Woodacre, eventually dropping in to Olema. Weekend traffic on HWY 1 can be thick, but weekdays are not bad. Another way to get to the coast is to take Novato Blvd. through Novato, and when it finally dead-ends go left and head toward PT. Reyes Station. On the way you can stop at the Marin French Cheese Factory, which is a nice spot of a snack or picnic. Speaking of cheese, Cowgirl Creamery in Pt. Reyes Station is worth a visit.
I'll add some places to visit next.