Add a piece of foam or rubber under the pump for starters. Isolating the pump from the floor often takes care of a lot of the noise. If the PEX lines go directly to the pump you can also add some short flexible supply lines between the pump and PEX. One or both should take care of the problem.
Actually the pump should have rubber bumpers under the feet where it fastens down to the floor. Some times these screws get tightened down to much. When that happens it defeats the purpose of them being there.
I agree with John's post.
2008 Cruiser CF26RK
2013 Ford Eco-Boost
Heavy duty payload - Max tow
Try putting some foam pipe insulation around the pex water lines in the compartment where the pump is. Those lines vibrate thus rattling make noise. You may also want to upgrade to a higher quality quieter pump.