July through October is prime whale watching season here. It's when the Humpbacks and Blue Whales spend time fattening up on krill off of the coast of Northern California before heading back down to Baja to breed. A trip to the Farallon Islands, 27 miles west of San Francisco, can be one of the best ways to get up close to these giants of the sea.
You can get out to the Farallones on tours organized by SF Bay Whale Watching, which depart early in the morning from Fort Mason (weather permitting). The two hour haul to the Farallons is a bit harrowing, which is to say strong stomachs, sea legs (and potentially Dramamine) are required.
Helicopter in Morgan Freeman and Sigourney Weaver- we've got a real-time episode of Planet Earth on our hands. More than 20,000 California gray whales (and a smattering of humpback, blue, and killer whales) are making their way along the Northern California Coast (en route from Mexico to Alaska) for their annual migration (in March and April). Dozens of pods per hour (each pod contains 20 or so whales) will be swimming by at a rate of 70 to 80 miles per day. Their journey -- one that should make you think twice about complaining about your next half marathon -- is 12,000 miles, the longest known distance that any mammal migrates on an annual basis.