How to fix small wobble in rear wheel? My rear tire has a small wobble that I have not been able to get rid of.

When you put the bike on its back, and spin the rear wheel you can notice that it moves about 3mm to one side once every rotation. The small wobble causes series discomfort when braking from high speeds (I have disk brakes) since it makes it feel as if I am braking hard once per rotation causing me to jerk back and forwards a bit.

Any idea on how to fix this?

I have taken the wheel off and ensured that it was correctly aligned, yet this did not help.
Because you said you have disk brakes, it is unlikely that the unevenness is in the rim/tire. It must be something at the hub. Because you said it is visible at the rim, it is not a bent brake disk (unless you have both rim and disk bent). It is also unlikely to be loose bearing cups, though I would have checked them as well. When the wheel is not rotating, try to wobble it sideways with your hand. If it does wobble, tune up the hub.

The last possibility is that the wheel's axle does not sit properly in the dropouts, i.e. it is not installed correctly as the whole unit. Loosen the quick release skewer or nuts that hold the wheel and make sure that you've pressed it all the way in the frame's dropouts before closing skewer or tightening the nuts again.