The first thing I'd do here is take it apart and clean everything, especially the impeller and the related areas.
Dirt and other stuff can really cause noise issues.
What is the name and model of the pump your using? Some are know to have noise or vibration issues.
I use one of them on my closed loop in my reef. It's a good pump.
That is one of the down sides of these DC controlled pumps. Most of them are made in China, and once they make the run, that's it for them. Even when you get it new, replacement parts might not be available. The good news is that most of these pumps are similar, so if you can match the specs, replacement should just be a swap. (Famous last words, I know)