Using CD4093 as Schmitt trigger oscillator. How to measure high and low trigger thresholds?
You can change the channels to DC coupling to (at least approximately) directly read the voltages. Touch the probe to ground and to a known voltage such as Vdd to determine the zero point and the calibration. That should get you within 5% or so. 



To get a more accurate reading, you could monitor the output of the gate with something like an LED (at low current so as not to affect the supply much). 

Then use a pot (preferably multi-turn such as a 10K 22 turn trimpot) across the 9V supply, with a low pass filter (eg. 100K and 1uF film or ceramic) and carefully sneak up on the transitions, monitoring the voltage at the gate input with your DMM. You should be able to get within less than 1% that way, but it will take more time. 

The transition points will be somewhat sensitive to temperature and very sensitive to the supply voltage (and therefore to any ripple on the supply voltage) so a good bypass near the chip (eg. 100uF electrolytic in parallel with 100nF ceramic) is called for.