Whaling was a big deal in San Francisco Bay. The first American whaling ships in the Pacific showed up in 1791 but mostly stuck to Hawaii. In 1858 the Pacific Oil and Camphene Works opened in San Francisco to process spermacetti and sperm oil. During the gold rush years, captains avoided San Francisco to avoid losing their crew, but by 1885 and until 1905, San Francisco was the busiest whaling port in the world. 40 ships annually ventured up to the Arctic Ocean and came back with whale bone and oil. Whalebone prices collapsed in 1908 and all the ships of the conglomerated whaling industry group Pacific Steam Whaling Co. were shuttered in 1910.
Occasionally grey whales would venture into San Francisco Bay, but mostly they were out along the Pacific coast.
 San Francisco Bay - A Pictorial Maritime History, Page 107. Oakland History Room.