How to implement step-up DC-DC converter with reverse current capability
Can I simply connect a Zener diode in reverse in parallel with the
  boost converter, which breaks down at some voltage above 36V, e.g.
  37V?


You can do that, but it won't have any effect unless the motor is being mechanically driven at higher than normal speed. 

To brake the motor you can switch a resistor across it. The lower the resistance the more current the motor will drive though it, which produces the braking torque.  The resistor must be rated to take the average power generated.


  I am looking to return about 100 watts for 1/4 of a second, once every
  second.


Not sure what you mean by 'return' but at 100 watts and 36 volts the current would be  100/36 = ~2.8 amps. Some voltage will be lost across the motor's internal resistance, and as it slows down it produces less voltage, so the peak current for an average 100 watts of braking power will be higher. 

The braking circuit could simply consist of the resistor and a suitably rated power MOSFET connecting its lower end to ground. However if the brake is turned off before the motor stops a positive voltage spike will be produced by the motor inductance. The Zener diode would help here.