So if I understand correctly you are saying that the noise is introduced upstream from the amplifier in the signal path...which is typical. Run the EQ without an input source and see if the noise is back. If no noise then run an ipod on its own battery power into the EQ and without the HU. If no noise then re-connect the HU. Run the HU directly into an amplifier totally bypassing the EQ. Try running the HU speaker level out into a speaker level input on the amplifier instead of using the HU RCA preouts. You could have a bad preout section on the HU. The point is you can isolate and eliminate each potential cause.
None of this will be particularly revealing until you confirm that the HU, EQ and any other in line processor references the identical ground and supply as the amplifiers. Also, try grounding the EQ and HU chassis as well as the ground wires.