We were there last September and loved it so much we will be going back this fall again. We stayed in one of the campgrounds, but at that time of year, we were the only ones. Had it all to ourselves. We drove the entire byway and saw many boondockers along the way with much larger units. I could not tell you exactly where other than they were south of Boulder Creek CG. Using Google Maps, type in Boulder Creek Campground and Picnic Area, Wise River, MT, using satellite view, follow along the Pioneer Mountains Scenic Byway and you'll see some boondockers to the west of the highway and other roads much further down to the east.
Check out Campendium as well as this has a lot of info on various campgrounds. Again type in Wise River, MT and the campgrounds in that area will come up. No free sites appeared on this site though, but there are boondocking sites that may like FreeCampsites.net.