Most Ontario bylaw have provisions stipulating that property owners can prune tree branches extend over their property line, with one exception that the tree has some special significance. Confirm with your municipal office. Out of courtesy, you may consider leaving a note to your neighbour before you take action.
Second, you do have the right to the air space above your backyard to a reasonable extent, for instance, flight path is beyond this resonable extent but you have every right to stop someone from flying a drone over your backyard, letting alone the trees.