We are not into the huge amusement parks, especially with children as young as yours, so of what you suggested, I would vote for Santa Cruz Beach Boardwalk. Six Flags is my least favorite with younger kids. It is huge, therefore exhausting to navigate, a pain with strollers that aren't allowed past certain points, many rides are off limits to smaller kids, it is really crowded, hardly any shade and a very hot location, and it seems more of a money pit than the rest of them. I see most people disagree with my experience but that's how we feel about it.
I can suggest a lovely hidden gem for young children in Gilroy, called Gilroy Gardens. It is an amusement park for children up to about aged ten, although older children and, especially adults of all ages seem to love this place. You may want to look it up online. It is large enough to navigate in a day and has loads of variety with the rides and attractions but it is less commercial somehow, very pretty with rides set amongst beautiful trees, (the trees have been especially designed and very interesting), and gardens, waterfalls and pretty scenery. There is a lovely water park area in the summer and cool Christmas lights and an ice skating rink in winter. There are mellow rides and fast and fun roller coasters but none that would scare the pants off of a daring teenager.My kids think it is the best place on earth!
If you'd like more information about it, other things to do around there, or ideas on where to stay down there, I could help you out as I have family who live down there and know everything about it all. If so, please private message me.
Good luck and I hope you have fun wherever you decide to go!