Hi, well regarding the SF tour I was going to mention two of the ones I have seen the most in San Francisco. I live about 45 minutes away but I went to school in San Francisco and was there all morning and day about 4 days a week for 3 years, just finished a few months ago. The two tours that I would see everywhere!, are:
http://www.city-sightseeing.us/
and
http://www.buysanfranciscotours.com/tours/san_francisco_cable_car_tour.html
The first one is a double decker bus, and the 2nd one is a Cable car on wheels. I believe they only stay within the main touristy district of San Francisco, I'm sure the website will have a route map. And speaking of maps, also wanted to mention, that it's not really necessary to purchase a map of San Francisco. There are plenty of FREE booklets scattered all throughout the city that have excellent detailed maps of most of San Francisco, even includes street names, touristy points of interest, and bus routes.
The booklets also have lots of coupons, points of interest information, and more information regarding tours to additional places including Yosemite and Muir Woods. The Caltrain train station will have them for sure, but they're also located in newpaper stands, local shops, hotels will probably have them. I've never been to it, but there is a Visitor Information Center on Market Street:
http://www.onlyinsanfrancisco.com/plan_your_trip/vic.asp .
The booklets look like this, and they are on the small side so very portable:
Here are some of the websites listed on them that may help with information (I have not linked them):
BayCityGuide.com
SFGuide.com
MapWest.com
SFTravelCoupons.com
Pier39.com
Guideyou.com
BlueandGoldfleet.com -- this is pretty fun, will take you under the Golden Gate Bridge
Lots of coupons to be found in the booklets so have a look at them first before you go anywhere. And a few free museum admission days to note if you'll be around:
~The California Academy of Sciences is free the 3rd Wednesday of every month.
~ Asian Art Museum is free the 1st Sunday of every month
~ Legion of Honor is free the 1st Tuesday of every month
~ The Exploratorium is free the 1st Wednesday of every month
~ San Francisco Museum of Modern art (a.k.a. SF MOMA) free the 1st Tuesday of every month
~ Forgot about the De Young museum: First Tuesday of each month is free
and most of these places will offer a senior or student discount, so if you have a student traveling with you (regardless of age) bring along a Student ID.
Have fun!