Have you tried putting something like styrofoam or sponge between the HOB and the glass, or wrapping the electric cord in some sort of dampener material? Where is the sound coming from?
Also, this may be heathenous of me to say, but I turn all of the noisy equipment (air pump, filters) off at night in my bedroom so I can actually sleep....maybe it might be worth it to run the skimmer only at night?