I have 2 parents (60) with me, need the best route in San Francisco to cover these?

All of those things are fairly close together. Ghirardelli Square is at the western end of Fisherman's Wharf. Pier 39 is at the eastern end. They are about a mile apart. The boat for Alcatraz is about in the middle. Your biggest problem will be parking. It's hard to park anywhere along there. There is a streetcar (not a cable car, but an antique streetcar) that runs up and down the wharf, so you might be able to park in one place and take the streetcar from one end to the other. Coit Tower is not on Fisherman's Wharf but close, at the top of Telegraph Hill. And there again, the parking situation is horrendous. There are about 20 parking spaces at the top of the hill and they are always full--in fact you sometimes have to wait in line for 20-30 min. just to get to the top of the hill because everyone ahead of you is waiting for a parking space. If you're young and hardy, you can park at the bottom of the hill pretty easily and climb up. Your parents probably won't be interested in that though.

Cable car covers all within 3 blocks.