Put the index as a whole:
a[[x, y]] = a[[y, x]]
With your example:
a = np.array([[4,3,1], [5,7,0], [9,9,3], [8,2,4]])
a
# array([[4, 3, 1],
# [5, 7, 0],
# [9, 9, 3],
# [8, 2, 4]])
a[[0, 2]] = a[[2, 0]]
a
# array([[9, 9, 3],
# [5, 7, 0],
# [4, 3, 1],
# [8, 2, 4]])
