We struggled to find somewhere in San Francisco that offered parking, in what's considered a 'safe' area, and at a decent rate ... Fortunately after deciding to try somewhere for just one night and see how it was, rather than booking for all three, the Lombard Motor Inn came up in search results. It had a room available for two nights but not all three, but a different type of room available for the third night which is why it hadn't shown up as available when we searched for 3 nights - so we called up to check and they could accommodate us which was great.
We were very skeptical of what it would be like when we arrived around 8pm, and were worried there would be no parking spaces left. But there was and actually they had a decent number of spaces. The check-in desk guy even let us park in a space that's normally coned off but because we had a compact car it was fine. He was really friendly and welcoming, and very helpful answering all our questions. Our room was also great. Large bed, tv, safe in the wardrobe, sink outside the bathroom, and table with two chairs. We booked for the second two nights immediately.
There was no breakfast but we were out everyday anyway. There was free wifi. Easy walking distance down to the waterfront, Ghiradelli square, and marina area. There's a launderette nearby called Greenwich Clean Time which was ideal because we were traveling for 2 weeks and had almost run out of clean clothes! Taxi from Union Square area one night cost us $12 inc tip.
We only had one hiccup after the second night stay, we came back in the middle of the day and our key cards didn't work. We knew the carpets were being cleaned that day so had thought it was to do with that but when we go to the desk they said we were meant to have checked out. There was obviously a mixup when we'd booked the extra two nights stay but fortunately they could still accommodate us and hadn't moved anything out of the room.
Road noise wasn't too bad, but it wasn't completely cut out when you shut the balcony door. We were fine sleeping through it though and not a road that's too busy at night.
Overall good accommodation and decent value for money. Definitely recommend.