With Flyback Diode, still have spike.
It surely depends on how it is measured. The following 2 images from TI are quite helpful on measuring noise/ringing signals:





These images represent how to "probe". Note that a long ground cable of the probe can pick up a lot of noise from outside.



There are also some other things to consider: 

- Insufficiently Bypassed Supply Line: It's also quite important to bypass the supply line at higher frequencies. I would put 1-100nF capacitor(s) across the supply line as close to the point where the motor is supplied as possible.

- Stray inductances: Sad but true. Although it's hard to say without seeing the setup there should be some stray inductances coming from the setup/layout. The tracks/cables from positive supply line to motor, from motor to mosfet, from mosfet to ground, from motor to diode's anode, from diode's cathode to motor etc. All create some stray inductances. So, keep those tracks/cables short as possible.

- Bad/insufficient/weak gate drive: Sorry but schematic does not show anything about this. If the gate has a series resistor then put a fast diode (e.g. 4148) parallel to this resistor in a way that the anode is connected to the gate and the cathode is connected to the PWM source. This helps to turn the MOSFET off faster.

- Capacitor Across the Motor: Try putting a lower than or equal to 1nF ceramic capacitor right across the leads of the motor.

- dv/dt of the Diode: I'm not sure about this but I think other experts may enlighten.

If there are spikes after fixing/improving these issues then put a snubber across the drain and source of the MOSFET. This document is quite helpful on designing snubbers.