Maybe easier via ax.text(…):
from matplotlib import pyplot
from mpl_toolkits.mplot3d import Axes3D
from numpy.random import rand
from pylab import figure
m=rand(3,3) # m is an array of (x,y,z) coordinate triplets
fig = figure()
ax = fig.add_subplot(projection='3d')
for i in range(len(m)): #plot each point + it's index as text above
ax.scatter(m[i,0],m[i,1],m[i,2],color="b")
ax.text(m[i,0],m[i,1],m[i,2], '%s' % (str(i)), size=20, zorder=1,
color="k")
ax.set_xlabel('x')
ax.set_ylabel('y')
ax.set_zlabel('z')
pyplot.show()
