I remember this sort of problem from years ago, with screw-on clusters. Is yours a steel or alloy hub?
It's not a bent axle, as the axle stays fixed, so the hub will not vary in its position as it rotates.
Lower quality pressed steel hubs can develop a deformity of the hub shell/flange as a result of heavy loading, I believe. Alloy hubs are generally built stronger (forged) and are less prone to this deformation. The deformation causes the freewheel boss to be misaligned with the wheel centre-line, and hence there is a wobble as it turns.
I'm not sure about the repair options, but for cheaper steel hubs the best answer was a new, better quality hub

It could be upgrade time

Of course if your chain runs well, and shifts correctly, just keep riding it.
If it's a cassette hub then I don't know what you've done

Riding bikes in traffic - what seems dangerous is usually safe; what seems safe is often more dangerous.