I'm no expert on the symptoms of ball joints on Lexus, although on other cars I've had I would expect a worn ball joint to clunk or bang over sharp bumps. I wouldn't expect it to cause vibration particularly, but would amplify any vibration caused by something else. As far as tyres go, I wouldn't expect them to cause vibration either unless the tyre is damaged in some way. A worn ball joint may wear them unevenly if it was bad enough I guess. Hopefully someone else will have first hand experience of warn ball joints on a Lexus.
The only bad vibration issues I have had with my Lexus (Mk1 GS300) has both times been caused by a seizing calliper, once on the rear and once on the front. When the front one was sticking on (last week), the judder was horrendous and was made even worse under braking. Might be worth a look to see if this is a problem on yours.