We don't know what kind of budget you are on. We could make better recommendations if we knew.
Union Square would put you right in the middle of things if you are going to be getting around without a car. I used to work for that Victoria's Secret in the lobby of the St. Francis Hotel. I loved that hotel for its historical value.
My customers at the Cliff House rented rooms out there when they wanted some place quiet with nice views. The Seal Rock Inn is not fancy, but it was popular with people who wanted to wake up to the sounds of waves. Of course, it also puts you very close to the fog horns too so it is the luck of the draw there. People who wanted to see Sutro Gardens, Legion of Honor, etc. slept up there.
If you want the kind of rooms that you would encounter coming off of an Interstate highway, head over to Lombard Street. It has a bunch of motels all lined up in a row and a couple of diners like Mel's and the International House of Pancakes.
I don't know much about the hotels and motels over on Fisherman's Wharf. My husband's friend used to work for the Sherton, which looked nice enough the brief period that I was in it. All I know is that it is very high traffic in that area. I have never worked over in that area but used to hang out there when I lived downtown. During high tourist season, there are lots and lots and lots of people on the streets day and night.