You have 4 great options and choices all are near to the Center of City and near Union Square, near city transportation, Cable cars, theaters, shopping, dining, art galleries, etc.
1. San Francisco Marriott Marquis - Good hotel, close to Art Museums, good hotel if you staying with Kids as well. Request upper floors with Bay Views
2. JW Marriott San Francisco Union Square – Good hotel all around, request room view views, (Do not wonder wrong directions into undesirable area)
3. San Francisco Marriott Union Square - Good location, modern type with large hotel rooms
4. The Stanford Court Renaissance San Francisco Hotel - Classy California Historic Hotel. smaller rooms, great restaurant, request room with views of the Golden Gate Bridge
If you want to stay close to Bay then check outSan Francisco Marriott Fisherman's Wharf it's a near the Piers and many of the related tourist activities as well.