Bay Cruise is good way to see the Golden Gate, Alcatraz, and the general San Francisco Bay Area when you have limited time, as it's a non-stop cruise. The cruise takes off from Pier 39, which like a lot of Fisherman's Wharf, is very touristy.
Inside and outside seating are both available on the cruise, and you can quench your thirst and hunger at the onboard snack bar. I suggest taking a cruise that sails during the sunset; the orange of the setting sun deepens the orange of the Golden Gate even more. I was able to take some excellent pictures.
For the $20 I paid, I was also able to see Coit Tower on top of Telegraph Hill, Ghirardelli Square, the Presidio, the Bay Bridge, and the sea lions on the pier - all from the bay. One day I'll go back and see all those places up close.
The cruise also provides a narrative, giving insight into the history of some of the landmarks you see from the boat.
I recommend the cruise if you have limited time. If you have abundant time, take a bike ride over the Golden Gate and the night tour on Alcatraz Island to get the best experiences.