First make sure the cause of the noise is not mechanical in nature (bearings, misalignment, worn bearings, lose hardware, lubrication, etc., etc.). If the cause is identified as being electrical in nature you can check some of these.
Is the motor rated for VFD service? Although you may be able to use a regular 3 phase AC motor with some VFD's, a regular 3 phase motor is not design to work with VFD's and thus will operate with higher electrical losses than a motor which is rated for VFD service and it is matched to the VFD. This translates to the motor operating at higher noise levels and at higher temperatures than the stated nominal values at the same RPM. Also, whether the motor is VFD rated or not, if it is being operated at a speed lower than its rated nominal speed it will naturally produce more noise due to the decreased PWM duty cycles required by the VFD to operate the motor at lower speeds. If this is the case you can use gear reduction to operate the motor at or near its nominal rated speed.
If the noise is something that wasn't there when the equipment was commissioned, then you may want to determine if the load of the motor increased for some reason. You can check the current of each phase and compare with the commissioning data (if available) or with the motor data sheets. You may be able to get the data from the VFD itself. Also check that the current in all the phases is the same. If a phase has a significantly different value than the other phases it is an indication of a problem with the VFD or the motor. If the thyristors or IGBT's of the VFD are miss-firing (depending again on the make and model of the VFD) it may also be a cause for increased noise. However, pretty much all the latest VFD's have differential phase current & voltage detection and will immediately trip.
Otherwise if you have spares, try by a process of elimination. If the noise is coming from the filter then replace the filter, next would be the VFD and last, the motor. Depending on the size of the motor it may or may not be easy to do. For example, on electrical propulsion vessels, the reactor weights several tons, so unless the drive is down, it will probably have to wait until dry-dock.