Discussion for all things Bay Area.
You might want to try Hoff St Garage, which is pretty close to Union Station. Mission isn’t the greatest area, but they have an attendant, it’s well lit.
Biggest piece of advice for parking in the city: never leave anything in your car. Heard horror stories where someone left their jacket in the passenger side and their car was broken into.
You can also put things in your trunk. As long as it's not visible.
+1 for Academy of Sciences. Nerd shit galore.
Academy of Sciences is good (and has parking if tmyou arrive early). Legion of honor is a good art museum and it's near other good sights.
Stanford has an embarrassingly large Rodan collection.
The golden gate botanical garden is large if life science is your thing.
I like muni. It's worked for us and is usually reliable. Depending on the route, pay attention to is you're getting on a regular or express. Some skip stops (and are faster).
Have fun!
One thing to consider is getting a larger ride share to & from a nearby BART, it may remove the worry about your vehicle if you're not confident in the garage situation. Not having to backtrack to the car may also free up your ability to explore esp. if you're using muni to get around during the day. I second your coworkers, if it can be avoided, leave the car, but that's just me.
For a recommendation, the palace of fine arts had some really well done escape rooms if you're into that sort of thing. I've done a number of escape rooms & the palace ones stand out as my favorites.
If you're all going together everywhere anyways, i strongly recommend using Uber/lyft
I think the Exploratorium is great, it's probably my favorite Bay Area museum. Check out the cable car museum if you're in the area, it's free and it's pretty incredible to see how these machines work.
Near Union Station, there's a paid parking lot under Union Square. The area can be a bit rough, but the cops are constantly patrolling due to the tourists. If you keep everything out of sight, you should be okay.
Land's End also has a parking lot that's free, which you can walk into the Presidio. Land's End by itself is pretty cool and worth checking out.
If you're going to be in Fisherman's Wharf anyways, I can recommend the Ghirardelli Square parking lot. It's pretty close via Muni to Exploratorium.
If you don't plan on having your car anyways, one thing you can do is park in the Daly City BART parking lot, and BART into the city.