You should DEFINITELY spend some time around Del Norte County in the Smith River Recreation Area (which is adjacent to the Northern End of Redwood National Park). If you have time to do some backpacking there, "Devil's Punchbowl" will blow your mind. As you go South, you should definitely hit up "Fern Canyon" or the "Big Trees Loop" in the stretch in Northern Humboldt. Also, where the Klamath River meets the ocean often has whales if you go in the winter time. It's a pretty spectacular vista from a hill up there.
The Eel River is beautiful, but you'll it's a little South of Ferndale. If you continue to drive south on 101, you'll be driving along the South Fork of it and lots of great swimming holes abound there. You should definitely also take time to go to the Lost Coast and the King Range. Head into Shelter Cover and do some hikes there or even more spectacular is to drive through Ferndale and enter the King Range from the North. It's stunning.
I would also say if you have some extra time, go into Round Valley and Covelo and go swimming in the MIddle Fork Eel. It's a spectacular river with amazing swimming holes and is rarely visited. You're almost guaranteed to see bear in the Yolla Bolly Wilderness, which is right there.
Small towns worth stopping in: Arcata, Laytonville, Ukiah, Willts, and if you go along HWY 1, Mendocino.
But as others have said, you can't go wrong. It's a spectacular area!