Alternator whine is caused by the varying current from the alternator causing varying voltage drops in wiring and across the battery itself.
It can be direct from the power connections of a device, or due to different things being connected to ground (battery negative or chassis) by different paths, with different currents in each.
Do you get noise from the amp with the audio inputs disconnected from the source and shorted out? If so, it's a power supply problem.
If not, it's due to different grounds (a "ground loop") and power filtering will not remove it - you need a input isolation transformer, not a noise filter. eg. Something like this:
https://www.rapidonline.com/AV-Link-201-086UK-High-Quality-Ground-Loop-Isolator-35-4561
Assuming you get noise with no input connection - you need to say exactly how the amp power connections are arranged and where power/ground are connected, with what size cables, where the amp is located etc. etc.
Also check the battery ground connections and any cross-connections / grounding straps between engine, chassis and battery negative are all clean and sound; if there is any trace of rust in any connection, they need cleaning and re-assembling with a coating of vaseline to prevent them corroding again. If any cables are starting to crack or fray, replace them - some cars use bare copper braid which can corrode over time.
Any slightly high resistance connection like that may make the problem worse or incurable.