We head up a bunch throughout the year and usually camp at the Lewiston Bridge RV resort (http://www.lewistonbridgerv.com/). We grab the nice campsites closest to the river and have been doing so for years. Nice and safe with great tree cover.
When we don't feel like freezing our a$$es off, we stay at the Lewiston Valley Motel (I can't find the website right now...

). It's right next to the gas station/Mama's restaruant and I think it might be the cheapest lodging in town.
That's all if you're fishing the upper river, of course. We'll be up there again in the beginning of November, so be sure to leave some fish for us...
My buddy and I camped down lower for the first time this past weekend at Big Flat, and that was nice too. All the Shasta/Trinity parks seemed pretty good.