We've always enjoyed driving the less-traveled route (US 395).
Definitely Crater Lake. There's a neat rock you can jump off of into the lake (more of an adult-sized jump) if you want the details. The campsites can fill up but are quite peaceful.
You might look into Lava Beds National Monument. Cool hikes Lukas would like, plus they'll give you flashlights and let you explore the caves on your own. They're rated for difficulty. One of our absolute favorites, and as we've often found with national monuments, a really nice campground.
Lassen Volcanic National Park is also well worth a stop, and coming into Yosemite from the back side (Tioga Pass) offers plenty of inexpensive, beautiful NFS campgrounds. Tuolomne Meadows has some nice hikes and is less crazy than the Valley side.
I'll dig a bit more in my AP and FB travel logs. End of Sep - Oct 2017 was our last trip that way (starts https://www.attackpoint.org/viewlog.jsp/user_1040/...
), plus another trip as far as SF maybe in Dec 2016 that was limited by snow road closures.