The City, as locals refer to it, can be tough with a heavy stroller, so keep that in mind. You may consider using two lightweight strollers as opposed to a heavy double. I used to live in Brentwood, CA a little over an hour East, so we went a few times when my kids were babies. When they were 3 and 1, we went with a huge Peg Perego double stroller & were miserable because we couldn't go some places due to the bulk and the hills.
Pier 39 is great for young families, there's a carousel, sea lions, and an aquarium. Boudin Bakery is a great place for sourdough and chowder.
Also, it sounds crazy, but the cable car museum is cool too. The last time I was there, this was free.
If you want to ride the cable cars, you need to catch it at the beginning or end of the line where they turn it around. One station is by Ghiradelli Sq. It is almost impossible to catch it along one of the stops as mostly tourists ride it & they ride it from beginning to end. Be prepared for long lines for this. The historic street cars are neat to ride too. I recommend buying a buying a Muni pass for the time you are there. It allows the most flexibility. If you don't you'll end up over paying for individual tickets. You can check the website sfmta.com for locations. The easiest one I've found is at Union Square.
Bocce Cafe in Little Italy North Beach is really good and reasonable. The ambiance is great, price is very reasonable and they have garden seating. Not as touristy as other places. My cousin introduced this to me when he was going to college in the city, I've been back at least 3 times since then and never disappointed. It's where the locals go.
If going to Alcatraz, be sure to buy your Alcatraz tickets in advance as they tend to sell out quickly. It can be really hard to get tickets the day of. Be on time for your boat or they might not be able to fit you in on a later boat.
A great hamburger place is In & Out Burger, a California institution. There's one at 333 Jefferson St. San Francisco, CA 94133. If you are not vegetarian, order the Double Double. You can also order a grilled cheese. It's not on the menu, but they'll make it for you.
Golden Gate is beautiful. When I left CA it cost $5 to cross, but it might be more now so be prepared if you plan to cross the bridge to Marin County.
Bay Quackers is fun. I've taken it in Seattle, but it's basically the same thing. You take the duck boat over land and in water. They pass out quacking devices and you quack all over the city. The kids will probably get a kick out of this. bayquackers.com
And to answer your question, YES it can get cold this time of year. Check weather.com and bring layers so you can take off and put on as the weather changes. Typical for this time is mild 70 ish during the day and chilly 50's at night.
PM me if you have any other questions.
K.
Mom to 3 ages 6, 5 & 3