Have you checked which power rail is the biggest problem? Consider adding linear post-regulators to the boost converters.
If you're adding LC filters like madires suggests, make sure that you're making a properly damped system. A low-ESR inductor paired with a low-ESR capacitor will ring at certain frequencies. Using a higher ESR inductor - or even adding some series resistance - plus a good old aluminium electrolytic will make it easier to avoid any such issues.