I had a similar problem and my dealer narrowed it down to the rca outputs on the deck were a little loose and not quite touching the internal board in the deck quite right. So it was creating a bit of an arc sending that nasty 'popping' sound to my towers. The popping also happened when I would hit big rollers or white caps the vibration from the jolt tweaked on the RCA's just enough to send that arc/popping sound.
They replaced the deck and it was good as new, no more popping. I did take us an entire summer to figure it out though
. The original deck was a kenwood 3248 (i think), definitely a kenwood, just cant remember model for sure. Good luck