Hi Cantona,
In regard to location I'd recommend that you would book a hotel in the Fisherman's Wharf area rather than downtown as a lot of the hotels listed as 'Union Square' / 'Downtown' are bordering the Tenderloin which is not a nice neighbourhood. The Wharf can be ott but its safe and close to boat trips around the bay and close enough to downtown to go in for shopping and the other attractions.
M