I also have clear memories of really bad mosquitoes in some campgrounds in N.S, but that was during the summer, family car vacation probably 20 years ago. Headnets and long sleeved tops and long pants are the only way to go when its like that--just as I had to do in Scotland in august 2 years ago.
Fall will be better obviously, although I would seriously look at weather patterns and such, as cold, windy, rainy weather could be a crappy experience. Winds are always going to be more prevalent out there, so do your research and have reliable full rain gear that you know works well.

also, I assume campgrounds close in the fall, so you'd really want to look into those details also, although B+Bs and whatnot are always going to be going (but colourful leaves Fall tourists could mean less availability also with these, so try to get an idea of how hard it would be finding last minute accomodation.