When it rains heavily I get a terrible leak around the chimney flue which enters the boiler in my basement (I think it's called the flue it's the piece coming out of the foundation wall and into the boiler). I have a chimney cap and inspected the crown of the chimney and the outside structure... patched a few minor cracks in the crown, but it still leaks... does anyone know what might be causing and how it can be repaired.

If the flue entrance is below grade you could have water entering from below grade level and no matter how much you try to stop the leak at or near the top of the chimney it will not work. I would dig down if necessary and find the problem. NOTE This is only if it is below grade for the flue opening.