Last time we were in San Francisco, we stayed at the Best Western Miyako Inn located on Sutter Street in Japantown. The Miyako is now called
HOTEL TOMO . We LOVED the hotel AND the location. Mike loved the "Japanese" breakfasts at the hotel's restaurant.
It's just a quick bus ride away from Union Square. You could walk it if you wanted to. Buy a San Francisco Transit Authority Pass and go quickly and easily all over the city without the nightmare and $$$$$ of trying to park.
Hotel Tomo has some great reviews on Trip Advisor. We would most definitely stay here again. The neighborhood is safe, doesn't have the panhandlers of downtown locations, and there's some wonderful places to eat nearby. Be sure to check out
HARRY'S BAR on upper Fillmore Street. It has terrific ambiance, terrific food and terrific drinks!