Some things you can do to calm annoying vibrations:
You could try just cleaning the flywheel. Of dirt. Might help.
Install a duct "skirt" "canvas duct connector" so that vibrations don't shake the structure as much.
You can try to "rebalance" your flywheel. Or replace it. Or replace it and the motor. Decreases vibrations.
You can add some padding underneath the furnace. A lining around the underside perimeter (if it's downdraft), or similar.
Could also add padding between the ducts and the wall.
If you want to be really aggressive, replace the furnace with a "two stage blower" then as long as it's close to temperature, it won't blow as hard. Or even variable speed even more so. But more expensive.
Some "normal" furnaces have an option for how fast they blow either "high high" or "high medium" so youc an vary the speed of the blower down a bit.
Or install radiant floor heating instead of forced air.
If your furnace hangs from the ceiling there are little rubber pads they can use to hang it with "compression fittings" that reduce vibrations.