Well the best way is probably using a thermowell that dips into the wort and allows a flexible thermistor to slide down inside the thermowell below the level of the wort. Also, a sanitized thermometer would work, but I don't want that in my wort while it is fermenting. If using a swamp cooler, I use the external water temperature and figure the beer to be anywhere from 4 - 8 degrees higher at full krausen when the yeast are chugging along.