Depends on where you use the car and a host of other long term plans for your car. Pillowball (or rose joints) are tough with near zero play and low friction. You'll also get the ability to use adjustable camber/castor tops with this type of joint. There are two downsides; as you have mentioned vibration/harshness passed through the body and the pillowball itself. This type of joint is susceptible to wear from hammering actions through the joint, which will cause the joint to snap or separate from it's housing. This failure presents itself as knocking first. Normal road use will likely not cause this, but things like pot holes, speed bump/jumps ect that would cause a hammering action through the joint will cause your coilover to fail prematurely.
The standard type rubber top mounts allow for a little more comfort, but no adjustability. These wear out eventually and do need to be checked with every service - they can stretch/tear/move in all directions. This is why they are not preferred for racing applications as any movement in suspension will change the wheel alignment during movement. This is all minor, and for road use will have no effect. They are mildly more comfortable.
I have used both in my car, I'm currently using the adjustable camber tops on my BC's because I don't drive it often and prefer the adjustability.
What kind of spring rates are you looking to use? Where are you going to use the car?
