Hey bro, First thing i would check is how its being powered. Is the Stereo Positive and Negative on its own battery, everything Stereo related, Deck, amps, EQ, everything has to be grounded on its own battery and powered the same way.

Second if you want to know if its the EQ or not then bypass it and plug the head unit directly into the Amps.

If you still get noise, what exactly is the noise sounding like? Is it the whine you get from an engine?
When exactly do you get the noise? All the time engine on or off? What about when you run the heater in the boat?

If the noise is a weird buzz, click click, buzz and its random that is commonly your Cell phone getting email, text messages or such and on Highend speakers, espcialy towers the tweeters actually pick these noises up.

On our boat unless im waiting on Claudia from work all cells are in airplane mode, this way i dont get that noise generated.

Let me know how it turns out.

Plus bro im only 30 minutes ride on the Vision to you, holler if you want me to come take a personaly look at it. Im in Salem every other month anyhow getting the oil changed on the bike. Carlton is closer then you think LOL.