For camping on Manitoulin, there's Batman(!) campground in (or very near) Sheguindah; a tent/trailer park at Vanzant's Point on Lake Manitou, just off 6, near Manitouwaning; I
think a campground in or near South Baymouth; there could be a couple more on or near Hwy 6, but I'm not sure. Last summer I stayed at a trailer park run by a cop in the community of Birch Island, ~20 kms N. of Little Current. He charged me $15. He said he was getting out of transient camping, but would make an exception for cyclists, presumably because we tourists are a behaved bunch. See
www.manitoulin-island.com To the south, on the mainland at Tobermory, there are 3 campgrounds (I believe Lands' End is one); and Happy Hearts camp. 4 kms south of there. But wait, there's more! From what a local told me, 2 campgrounds on Miller Lake, 30 kms (18 mi.) S. of Tobermory, off #6 a bit. And one right in Wiarton, on the waterfront. Oh, and there's a KOA just to the east of the town of Owen Sound; $24.
Now, I think stealth camping is doable in places; maybe somewhere along the Bruce Trail (a ~700km hiking trail from Queenston to Tobermory), which you'll be close by on the Bruce Penninsula. Possibly on Manitoulin here and there. PM me for more info on that.
For places to crash, I suppose if you ask someone nicely, they might let you set up on their front yard. I've never tried this myself, but people up there seem very friendly.
If you need an accurate, direct and quiet route from Buffalo(?) to Tobermory, I'll help you with that too. Cheers!
Edit: I'm positive I saw something about legal wild camping on Great La Cloche Island which is just across the 1 lane bridge from Little Current.