It's really challenging to find something nice for your family to stay under $100 in the SF area. Even though I live in the South Bay neighboring city of San Jose, I love staying at the Larkspur Landing Hotel in South San Francisco. Easy to get on and off the freeway if you have a rental. Then, there's always the train station. Haven't used it though. It is often used by commuters like my DH from the South Bay to downtown SF. Have you tried the Courtyard Marriott?