[frinkprof]

You won't find anything from the City (bylaws, even advice) that will deal with this situation, unless the tree (including its limbs) encroached onto City-owned land, which is not the case here. They will not get involved in such matters.

This is a civil matter between you and your neighbour.

If the tree is indeed encroaching (as you say it is) and if your neighbour wanted to take you to court, you would ultimately be on the hook for the costs.

EDIT: Roots only though, branches are more complicated, see below.