That's a problem right there. RG-6 isn't designed for use at audio frequencies, and the shield (since it's being used as an unbalanced return) is acting like an antenna.
You need to get some Belden 8451 (or it's easier to strip brother, 9451) from an electronics house. (Radio Shack used to carry a wire very similar, ask for two-conductor foil shielded cable.)
Connect it as follows: ( I'm assuming use of RCA phono plugs on each end)
Red wire: To tip on each end
Black wire: To shell (or "crown") on each end
Shield (bare)wire: To shell on one end only
. Important: Make sure the shield does NOT contact the shell at all on the end opposite this connection.
You may need to experiment, but connect the end with the shield tied in on the SOURCE end first.
That should eliminate most if not all of the pop. Also, a surge protector at the sub wouldn't hurt.
And if you have money to burn, you can always get Monster cable. It'll work well but is super expensive.
PM me if you have more questions/need more help.