Based on popularity and guest reviews, the best Bay Cruises & Boat Tours in San Francisco are: San Francisco: Inside Alcatraz Tour with Bay Cruise San Francisco: Golden Gate Bay Cruise San Francisco: Alcatraz with San Francisco Bay Cruise San Francisco: California Sunset Boat Cruise San Francisco: Skip-the-Line 1-Hour Bay Cruise by Boat San Francisco: Bridge to Bridge Cruise San Francisco Bay Sunset Cruise by Luxury Catamaran San Francisco: Skip-the-Line Escape from The Rock Bay Cruise San Francisco: Golden Gate Bridge Catamaran Cruise San Francisco: Golden Gate Bridge and Bay Sunset Cruise