Is the noise in the toilet bowl or the vacuum pump? The location of the pump would be the determining factor as to what type of insulation you use. Wrapping the pump might hold in heat generated by the motor, be mindful of that. You'll also have to consider that insulation might inhibit service and winterizing components. Are you thinking of wrapping the pump with soundproofing or just lining the compartment it's in?
Lots more information, perhaps photos, needed for accurate recommendations.
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Bob & Donna
'98 Gulf Stream Sun Voyager DP being pushed by a '00 Beetle TDI
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