How do we go about repairing/waterproofing the chimney?

you need to check the step flashing on the roof around the chimney......it may be lead..copper..or stainless steel......they are installed before the roofing tiles...they are bent and formed to sit on the roof then come up the sides of the chimney about 8"s...look for crackes that can be filled with a silicone caulk...or roofing tar.......the top of the chimney MUST be 10' horizontally away from the roof...other wise it may become a hazard with heating equipment ( down drafts)