As a Bay Area "local" and 5th generation Northern Californian I'm reading some of your pre-cruise plans with interest.
OK, I have never been to Alcatraz. In fact, I don't know any of my friends who have been either! I realize TripAdvisor says it's the number 1 attraction and I guess for tourists it probably is. I know that it is certainly not unusual to have a big landmark "right there" and have never visited. Gone around it, yes, stepped foot on it no. We also try to steer clear of Fisherman's Wharf, especially the restaurants and do not eat Chinese in China Town. I have been to the Winchester Mystery House when I lived in Silicon Valley. It's pretty kitschy and the drive from SF to San Jose is just not inspiring.
Now, these are just my two cents as I think there are far more interesting and/or unique things to do when visiting. if you have the time we have world-class museums but San Francisco is all about the natural beauty. Do walk around and explore.

If you have access to a car Muir Woods National Monument is an easy drive just 11 miles over the Golden Gate. You're sailing under the bridge, why not view it from above as well! Start early and then carry on and spend the afternoon in Napa Valley. No car and still want to get out of the City? Take a ferry to Sausalito (or Tiburon) for lunch and look back and enjoy the great vistas of the City. On your return wander through Ferry Plaza. It has some great restaurants and spots to enjoy uniques views of the Bay Bridge. Wonderful local oysters at Hog Island and outstanding Vietnamese at the Slanted door. Have a flight of wine at the Ferry Plaza Wine Bar.
I'm sure everyone knows that the Cable Cars are the only moving National Monument. We do ride them when we have out of town friends visiting. Don't wait in line with the crowds at the foot of Powell Street but hop on somewhere along the line.
The Bay Area has some of its best weather in September, so go ahead, play tourist, just enjoy!