Ramban (to Deut. 11:29) suggests that Mt. Gerizim is to the south and Mt. Eival to the north (which indeed is geographically true - presumably he had the chance to verify this firsthand when he moved to the Land of Israel at the end of his life), and in biblical geography the north is often identified with evil (as in Jer. 1:14Jer. 1:14).
(Furthermore, throughout Tanach directions are given relative to the east, making south the right and north the left; and again, the right is seen as the side of goodness and the left as the opposite - see Eccles. 10:2Eccles. 10:2.)
Another interesting possibility is that when you're standing in the valley between the two mountains, looking towards Mt. Gerizim puts you also facing Jerusalem, while looking towards Mt. Eival places your back towards Jerusalem. Perhaps, then, it was also meant as a veiled message that Hashem's blessings come when we make Jerusalem and the Beis Hamikdash the center of our aspirations, and the opposite when we abandon them, as sadly all six tribes standing on Mt. Eival - plus three of those on Gerizim - ended up doing?