If you want to see San Francisco in its entirety, Red and White Cruise is one of the best boat tours in the Bay Area. They tour pass the Golden Gate bridge all the way to Alcatraz. They offer many tours throughout the day. Word of caution, if you plan to ride outside on deck on the boat, it can get really windy so bring a jacket. Tours are not really expensive but coupons are always helpful in getting a good discount.
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