Masonry sealers do not create problems with chimneys, but it may not completely fix your moisture absorption issue. If the exhaust condensate has attacked the mortar enough to open up hairline cracks between the mortar & brick or make the mortar crown/dome on the top of the chimney extra-porous, a masonry sealer won't fix it- it would need new mortar. You should be able to figure this out when you clean the acidic exhaust-grunge off the brick.
I'm not sure if the Thompson product is really ideal for chimneys but it might be. There are some specifically designed for use with clay brick or chimneys. (LastiSeal, etc.) None are cheap- expect to pay $50/gallon or more for anything that will go the distance.
I'm not sure if the Thompson product is really ideal for chimneys but it might be. There are some specifically designed for use with clay brick or chimneys. (LastiSeal, etc.) None are cheap- expect to pay $50/gallon or more for anything that will go the distance.