Does it make the same noise when running but held in your hand? If so, some of what's annoying you is being transmitted to your case, which is then working like a speaker diaphragm. If this turns out to be the case, try sitting the pump on foam.
If you are using vinyl tubing, that can be transmitting audio power as well - put your hand on the tubing and see if the noise goes down - if so, think about using something lots softer, like silicone.
I've heard (but don't know) that these pumps make a bit less noise if you sit them on their "tail", so you could try that.
The noise that comes out of a pump is not distributed evenly - and you may have pointed one of the high output "lobes" either at yourself, or, more likely, at a reflective surface, like a case wall (which is also picking up some audio energy and re-radiating it on the outside (again, like a speaker diaphragm). Try turning the pump and try lining any hard interior surfaces with sound absorptive foam (the best stuff is for lining speaker cabinets and has a "limp wall" built into it - so in cross-section it looks like two layers of foam with vinyl between). You could build a separate box for the pump - remembering that it needs some airflow.
Finally, here's an off-beat one: you could try increasing the weight of the motor housing to bring the resonant frequency down (this works like putting a capacitor in a circuit, but you're working with mechanical energy and inertia). It was very common, years ago, to fill the ends of motorcycle handlebars with lead so they wouldn't vibrate so badly - particularly Velocette handlebars which, otherwise, had a tendency to "grow" in your hands.
Finally, if the noise is still driving you crazy, you might think about the Swiftech 650 - or a new one from DD as they're supposed to be quieter now.
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