It's relatively easy if both shaft sizes are the same,use the straight end of a steel rule lay it against the two shafts(piece of white paper behind) and you will see daylight on one of the shafts if there is misalignment, will be tricky though as you will have limited access below your table. If one shaft is bigger than the other put the straight edge on that one and just try to guestimate the run out.
Good luck
Mike