One way to obtain Greater Magic Essence is by disenchanting items in the 16 to 20 level range, more often from weapons than from armor. Above level 15, it can only be obtained from weapons. Another way to obtain Greater Magic Essence is by right clicking the Lesser Magic Essences, that will turn them into the Greater ones (conversely clicking on one Greater Magic Essence will break it into 3 Lesser Magic Essences). It takes 3 Lesser Magic Essences to make 1 Greater Magic Essence.