There are three options that I've done. One is an open, pay, lot that's a couple of blocks east on North Point (the street the hotel is on). It's fenced, but I can't remember if it's monitored at night. It used to be questionable for some people when the area just beyond the wharf was kind of questionable (believe it or not), but not anymore.
What I've done most often is, um, to park right out front on the street. If I recall correctly, the meters are "dead" from some reasonable time in the evening, and go "live" - e.g., have to be fed quarters - seven days a week - at 8:00am. The street is typically empty at night. (Well, weekends, and across the Christmas-New Year's holidays, are all I know about.) But I can't imagine why it'd be any different other nights, unless lots of people have caught on to this. You have to pay attention to the signs that say when there's night street cleaning, which, like most cities, is only one side of the street per night.
A third thought. If you are renting a car, most of the companies have outlets within a couple of short blocks of the hotel, should that give you options re keeping a car or not during your stay. I haven't paid a drop surcharge for picking up or dropping a car there, or at the downtown locations around Union Square, and/or at the airports (SFO, OAK). Actually, it can be a viable choice for transportation to/from the airport for several people at once. Then you can cab and cable car around town, saving daily rental fees, insurance, taxes & local fees, and, yes, parking -- not just at the hotel. Then walk across the street and get your next ride for ranging further out and to get you back to the airport. [The big picture: Cars only at the beginning and end of the trip. But that's another thread...]