Any square lies on a plane.  When that plane slices the cone, the intersection is an ellipse, call it E.

Now slice a second plane through the cone perpendicular to the cone's axis and containing the center of the ellipse.  That plane intersects the cone in a circle, call it C.

The diameter of C is equal to the minor axis of E.  The inscribed square in E is larger than the inscribed square in C.  But in order to have a chance to be larger than the square inscribed in the base, the major axis of E must be longer than the diameter of the base.

But increasing the length of the major axis of E requires tilting the slicing plane increasingly steeper against the base, which has the effect of shrinking the minor axis.

So based on this handwaving argument I conjecture that the largest square is the square inscribed in the base, regardless of the values chosen for the radius and height.