I am shocked you never heard the old quote attributed to Twain: The coldest winter I ever spent was a summer in San Francisco.
Not true that Twain said it, per snopes:
http://www.snopes.com/quotes/twain.asp
But, it is true that there are many cold, foggy summer days in the City by the Bay!
One or two other people have mentioned Cavallo as well.
Not in San Francisco, but as close as you can get! Plus Sausalito / Muir Woods / Stinson Beach are nearby.
My kids always liked going to the lighthouse when they were the age of your child too:
http://www.nps.gov/goga/pobo.htm
For what it's worth, Cavallo is highly ranked by T&L readers. I have never stayed here, but it is one of our go to spots for fabulous dinners.
http://www.cavallopoint.com/
"Cavallo Point Lodge Among World's Top Hotels According to Travel + Leisure Readers
Visit and Enjoy a Nature, Nurture, Culture, Adventure With the New Adventure Package
SAN FRANCISCO, CA--(Marketwired - Jul 16, 2013) - Cavallo Point Lodge ranked among the top 100 resorts in the world, and the top five in the U.S. according to Travel + Leisure's 2013 Readers' Poll. The lodge was the only Bay Area-based hotel to make the list, and one of only two in the state of California. The publication's World's Best Awards announced on July 2, named the lodge the No. 5 readers choice for a resort in the U.S., and No. 59 in the world. For its 18th annual poll, Travel + Leisure asked readers to cast their votes for the destinations, hotels, and their characteristics including rooms/facilities, location, service, restaurants/food and value.
Across the Golden Gate Bridge, Cavallo Point is the perfect place to enjoy nature, nurture, culture and adventure. This recent honor is just one more reason for travelers to visit the lodge and take advantage of its new Adventure Package, offering accommodations, a $100 resort credit each night, breakfast for two each morning and a picnic basket for two. The package includes options for seven add-on adventures on land, sea and air. Guests can also explore scenic trails for hiking and biking and the best of the Bay Area from Cavallo Point."