Maybe you can take out all the electronics out of the speakers, loose the speakers, then put the guts into a separate box or the sub itself. Then swap the 3.5mm jack with a RCA plug. Some RCA plugs come with a nut, so you can screw it into a drilled hole. I guess you can do the same with the volume pot, because most pots have nuts. Then you can put a nice knob on the pot.
Most active subs have a low-power RCA plug input, and most new audio amplifiers come with that output. I'd go for RCA.