Wow! This is not a good thing you have goin’ on here!!!
First…
Is the chimney all brick, or just a steel-sided “box” going up the side of the house??
Most likely, there’s some bad metal flashing and/or sealant around where the chimney comes through the roof.
Also…
At the very top, if it’s a masonry cap, the mortar/cement should be sloped away from the metal sleeves of the pipe.
Further…If it’s been leaking a while, you could be soon developing mold between walls if some of the leak is BEHIND the walls! This happens more than you think.
The Builder…You’ll have to have them get after any subcontractors. You must have some kind of warranty period with the builder.
Hope this helps!
Faron