Voltage regulation vs relative voltage tresholds?
What you should do depends on how you are driving the NTC thermistor.

If you are sensing temperature using a voltage divider formed by an NTC thermistor and a fixed resistor, then it will definitely work better to use a voltage divider for your switching threshold also. Both dividers should be connected to the same voltage. You can consider using capacitors in parallel with the resistors to improve the bandwidth of the voltage dividers if the voltage has a lot of ripple.

But if you are sensing temperature using an NTC thermistor driven by a constant current source, then you would be better off using a stable reference voltage for your switching threshold.

A hybrid option would be to create a low noise voltage rail (could be 3.3V from an LDO) to drive your NTC thermistor divider and your comparator divider. If the main voltage rail is very noisy, or if you need the utmost in precision this may provide more reliable operation.