Selecting Voltage Divider Resistor and OpAmp For Temp Sensing With NTC Thermistor
Probably you should use the mid-range-interest resistance. The exception might be if you were willing to give up some actual performance to make the temperature display look better at room temperature, with a low-resolution ADC.

Noise can be mitigated with a simple RC filter - temperature is a slow variable. 

Reference voltage is preferably the same as the ADC but really a thermistor typically changes around -5%/degree C so any "reasonably stable" reference will give you acceptable performance for your particular application.