Option A.) Order new windows from the manufacturer that are tinted. These zip into place.
Option B.) Various types of light films and wraps are suitable for Jeep plastic windows.
Option C.) Remove the entire top, lay it flat on the ground, and tint it like you would any other window. Remember to let it dry for at least 48 hours, then carefully put the top back on with multiple people making sure that the plastic windows do not bend or crease.