Prefer near BART or 1 mile from BART. Berkeley is OK too. I have low needs , just clean and no bugs. Hope to be around $150 a night or less.
Super 8 in Berkeley, 4 blocks walking distance to North Berkeley BART station, seems to be about $70 a night. Probably clean, but I haven’t stayed there.
When I’m in San Francisco, I love staying at the Hotel Kabuki. They run about $90-$160 a night depending on your bed preference and the rooms are awesome. Very clean, very great atmosphere. The only downside is they’re not near Bart. You can easily hop on over to the 38 bus stop which will bring you to the Market District, where there’s a bunch of Bart stations. On a good day, it’s about a 20 minute ride if I remember correctly. Perhaps someone more familiar with the area can give you a better time estimate.
Cheapest rate I see at Kabuki is $340 / night
I’ve stayed at Hotel Fusion several times, and it’s pretty sweet. The rooms are small, but very cute, none of that Hawaiian shirt/vomit bedding or carpet, located downtown, and not at all expensive. No a/c in the rooms, but it’s SF, so you’ll never need it.
I’ve also stayed at The Mosser, which is super cheap, has very small rooms, but is cute and is right downtown. Note it can get hostel-y, meaning you can pick to have your own bathroom or use the shared one (I know nothing of the shared bathrooms because I don’t think so), so make sure you pick a room with a john in it! If you don’t care about that kind of thing, I’m sure you can save even more buy sharing a bathroom. It’s a nice place, doesn’t cost much, in a great location, no bed bugs.
Have fun.
Really? I just checked and put in 1 person and just…randomly chose the 12th-14th of the month and got rates from $90-$160. I dunno if that link will work for you but that’s my search I did.
yes really that is what I got for May 1-4 , guess they need to sell the rooms this month
May is tourist season, Feb is not
Wow, I’m sorry. :smack: I didn’t even think about on/off season. I guess I’ve been getting a hell of a lot better deal than I knew all the other times I’ve gone down there off season. It’s a nice hotel, but not $350 a night nice 
Be sure to do a google street tour of the location.
“downtown” can mean Tenderloin = winos on the right, street walkers to the left.
Having to step over winos to get to your hotel can put a damper on your mood.
I’ve hunted around a few times for something budget-friendly in the Union Square-Finance area when I head out to San Francisco in November. (Probably won’t make it this year, sigh.) Some of my thoughts, YMMV:
Hotel Metropolis: This was pretty good, didn’t seem too expensive. Neighborhood felt a bit sketchy.
Club Quarters: Better neighborhood, still a bargain.
Crescent Hotel: I kinda liked this place, and it was definitely affordable, but that was 2+ years ago, and last November I was walking around and noticed that they’d changed their name, again. You might be able to find them on Google street view, though - Stockton just north of Sutter, so close to the Grand Hyatt.
Galleria Park: Nice place, but less affordable than any of the others IIRC.
I hope you have a great trip!
I stayed at the Hotel Del Sol in November 2011, and had a very pleasant stay. A nicely redecorated motel, with a good free breakfast and free WiFi. Link: Boutique Hotels | JdV by Hyatt The rates were good. It’s not near BART, as I recall, but it is a nice, if long, walk to the Exploratorium. Which I couldn’t see because I was there on business and busy during the day when it was open. 
I might lose my Nerd License over that.
If you don’t mind a room that contains 2 bunk beds and may be shared with strangers (dpends on how many of you there are) then Youth Hostels may be a good solution. They usually only cost you about $10 to $20 per night.
I stayed in one 10 years ago that was walking distance to a BART station. It was clean and safe, mostly populated by young travelers but it’s not actually limited to the young. The area outside seemed safe enough. There was a lot of begging activity but nothing that seemed threatening.
I think it was this one… http://www.sfhostels.com/downtown
I came to mention the Hotel Fusion, too. Right on top of a Bart station, clean and nice, excellent services. Not brand new but very nice anyway, and right on top of everything. Less than $150 per night.
I wanted to mention, if you can afford it, the Hotel Kabuki is a great place to stay.
When I was in San Francisco I stayed at the Hotel Whitcomb. It was pretty basic, but it’s only about one block from the BART station. I was there during December a couple years ago, so it was around $89 per night, but I just looked up May 1-4 and it’s $149 per night for those dates.
I’ve stayed at the Royal Pacific on Broadway, right on the border of Chinatown and North Beach. Reasonable room rates, nothing fancy. The big draw for me is the free parking, which may not be an issue for you since you need BART. The Montgomery Street BART station is 0.8 miles away according to google maps.