The word "noise" can mean a lot of different things. What exactly are you getting? is it a buzz? hum? static? distortion? just not sounding good? engine noise?
A buzz or hum is probably a ground loop, which is probably caused by having your amp grounded in a different spot than your computer and head unit. The device above might help, but doesn't always work. Make sure you have have a solid ground connection on all the devices in your system(i.e. sand off paint, solder on a spade connector)
If it is just static and not sounding as good as you think it should, it might be the high level inputs. In my experience, high level inputs have always left a lot to be desired. Try temporarily connecting you computer directly to the amp with
one of these. If that works, you might want to try going without a head unit or getting a head unit with pre-outs.