Calling the roofer today (assuming the guy giving the estimate can make it out in the next 24 hours) will give the estimator a better picture of where the leak is occurring (unless this is a problem many months in the making and there are water stains to show the source of the leak).
Agreed with slowsol that slapping on sealant is only a Band Aid, and at best a short term fix. I had a chimney at a house where the real culprit was the mortar between some bricks that had eroded and led to a leak behind the flashing, and not only did I need roof work but chimney work as well.
The good news (if any) with a chimney area leak, to address the point lfrost125 made, is that the heat from the chimney will dry out that area pretty quickly and reduce the potential for mold. That is, unless this is a long-standing problem that is just now getting notices; if this has been going on for many months, especially in the months without using the furnace, you might have some significant rotting and mold up there.
One last bit of potentially good news: the problem may be exacerbated by the temperature fluctuations the past few days plus the heavy rain. I once had a problem with a leak near a skylight, and it only happened 2-3 times a year when it rained like hell after a warm spell in winter. The rest of the year it never leaked, even in the heaviest summer storms.