The surface alignment of lyotropic chromonic liquid crystals can not only be planar (tangential) but also homeotropic, with self-assembled aggregates perpendicular to the substrate, as demonstrated by mapping optical retardation and by three-dimensional imaging of the director field. With time, the homeotropic nematic undergoes a transition into a tangential state. The anchoring transition is discontinuous and can be described by a double-well anchoring potential with two minima corresponding to tangential and homeotropic orientation.