Here are some links to museums, books, websites and archaeological projects that kids will love.
Nearby places to visit
Kule Loklo Coast Miwok Village at Bear Valley Visitors Center, Point Reyes National Seashore
http://www.nps.gov/pore/historyculture/people_coastmiwok.htm
Near the Bear Valley Visitors Center of the Point Reyes National Seashore, there is a recreated Coast Miwok Village. You can go into the structures, and at certain times they have ranger led walks and other interpretive programs.
Petaluma Historical Museum
http://www.petalumamuseum.com/
The Petaluma Museum has several local Native American artifacts in the upstairs area.
Santa Rosa Junior College Museum
http://www.santarosa.edu/museum/
The museum is located on the grounds of Santa Rosa Junior College at the Santa Rosa campus. it consists mostly of Native American artifacts and art objects including a large collection of Pomo baskets.
Other places to visit
Rosicrucian Egyptian Museum, San Jose
http://www.egyptianmuseum.org/
This museum is full of Egyptian artifacts. They also have several mummies, and a life size replica tomb you can walk into.
Indian Grinding Rock State Historic Park, Pine Grove CA
http://www.parks.ca.gov/?page_id=553
The park is located near Jackson in the Sierra foothills. There is a museum and recreated Native American structures, but the most interesting part of the park is the outcropping of marbleized limestone with some 1,185 mortar holes. It is really an amazing site.
Marshal Gold Discovery State Historic Park, Coloma CA
http://www.parks.ca.gov/?page_id=484
Coloma usually draws visitors interested in California's gold rush era, however, it also offers some insight on California's prehistoric history. While kids can try their luck at gold panning, there are also a several boulder outcroppings with bedrock mortar depressions. Nearby there is also a a group of reconstructed Native American dwellings.
Elden Pueblo Archaeological Site and Field Schools, Flagstaff AZ
http://www.fs.usda.gov/detail/coconino/learning/history-culture/?cid=stelprdb5350363
Several programs are offered at this archaeological site in Flagstaff, Arizona. They have classes during the summer for all different age groups, and host a filed school where people of any age (under 18 with an adult) can sign up to learn about archaeology and dig for a week or two in the summer. They have a low enrollment fee and allow free camping at the site.