Hotel rooms in SF start at about $65 per night at a not so nice place in a not so good part of town. Pier 35 is near Fisherman's wharf and most of the major hotels in that area are going to be in excess of $160 per night.
I personally would not want to stay in the Fisherman's Wharf as it is kind of out of the way to the city center.
For your first visit Union Square is probably the best place to stay. There are lots of good restaurants, shops, theaters and clubs in the Union Square area. It is centrally located with lots of public transportation options and within walking distance of most of the tourist areas. It would be less that $10 for a cab ride from any Union Square hotel to the Cruise Ship Terminal.
Joie de Vivre http://www.jdvhospitality.com has several hotels in the Union Square area in different price points. Each hotel is unique and they have a cool free program where they match you with a local person, called a Golden Gate Greeter, who shares your interests to spend a few hours with you and familiarize yourself with the city. http://www.goldengategreeter.c...
And for some great ideas of things to do check out these websites:
http://www.jdvhospitality.com/thingstodo...
http://www.mistersf.com
And as always a good way to check out a hotel before you check in is http://www.tripadvisor.com
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