Are there known cases of an airline pilot's becoming incapacitated, while in command of the aircraft, during a critical flight phase?
Here are a couple of examples from two studies that have a lot more detail and background information on pilot incapacitation in general.

From an ATSB study:


  After a normal touchdown, the first officer became unconscious at the
  flight controls and the aircraft began to veer to the right of the
  centreline. The captain took control of the aircraft to return to the
  centreline and completed the landing


From an FAA study:


  A 45-year-old B-737 first officer experiencing an alcohol withdrawal
  seizure suddenly screamed, extended his arms up rigidly, pushed full
  right rudder, and slumped over the yoke during an approach. The
  aircraft descended to 1,000 feet above ground level in an
  uncoordinated turn to 25 degrees angle of bank before flight
  attendants could pull the first officer off the controls, allowing the
  captain to recover the airplane