Wheels inofthemselves make relatively little difference for road vibration. The only ride quality difference is that tubeless tires may ride very slightly better which may require new wheels. Lowest hanging fruit is to run the widest, most supple tires you can at the lowest pressure that you reasonably can. Running latex or superlight tubes might help a very small amount. Bar tape can also help, and seatposts actually deflect a lot on road bikes and vary pretty considerably in how compliant they are, so that may be worth looking into. Saddles vary a fair amount regarding deflection as well. A carbon handlebar might make a very slight difference as well.
If you want a really compliant riding bike, get something that can run significantly wider tires. They are much more comfortable, are more versatile, and their only concessions regarding speed are pretty much a minor aerodynamic and weight penalty.