There are a ton of great hotel options in San Francisco, below are just a few we have heard good things about.
Hotel Rex - Stef's company uses this hotel often for out of town guests. It's right near Union Square.
Marriott Hotels - There are a number of Marriott hotels here in San Francisco. Jon's mom has stayed at the Fisherman's Wharf Courtyard location and had a very good experience. If you prefer to be downtown, there are a number of branches near Union Square.
While it is easy to get a regular taxi at the airport, car service mobile apps like Lyft or Flywheel are the easiest way to get around in San Francisco as taxis are scarce and parking is tight. We recommend Lyft and use it all the time. Flywheel uses traditional taxis and is a good choice too if you prefer a bonded taxi. You can download both apps on your iphone or Android phone.
Download Lyft here: https://www.lyft.com/app
Download Flywheel here: http://flywheel.com/
If you do drive, we recommend valet parking apps since spaces and lots are rare. They will meet you at your car, park it while you are busy, then bring the car back to you when you are ready to go.
Popular valet parking apps include:
San Francisco is a wonderful city, we love living here! Note that the weather here in January is like fall on the east coast, so we recommend that you dress in layers. Here is a great list of local attractions: