I used to use "Osborne's Maneuver", as detailed by Guy Lautard. You touch one side of the rotary table, and then move exactly half the diameter of the table. Then repeat on the perpendicular axis. Then repeat both axes. Three passes gives a neglible error. I now use a co-axial indicator on the centre hole:

I also set the rotary table to zero and align the T-slots to the axes of the mill; makes it a lot easier when cutting to specific angles. Of course all the methods assume that the rotary table, any centre hole, and the axis of rotation are concentric.
Andrew