I have some doubts about some explanations here. First, it are the wheels that are balanced, not the wheel/tyre assembly. Because the two wheel halves are not perfect symmetrical you have to balance that. But tyres wear, and some inbalance can occur. We've had that many times on nosewheels, when the left is worn to limits and the right is perfect, you get shimmy. But only in the case of unmatched wear. And mechanics will normaly change nosewheeltyres that are not matching. So if someone says here that you feel it every takeoff, I doubt it had to do with tyre wear. Second, the antiskid will activate the brakes before gear retraction, but this is to PREVENT high stress and vibrations. so I cannot see why they CAUSE vibrations.
I also don't believe that it can be worn wheel bearings, as bearings get changed together with wheel change, and this is quite often.
My guess the vibrations are just due to changing aerodynamic flow around the wing/body/empennage during rotation, just as extending flaps/gear/airbrakes cause more turbulent flight.