Use the following code it worked for me:
# Create the figure
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# Generate the values
x_vals = X_iso[:, 0:1]
y_vals = X_iso[:, 1:2]
z_vals = X_iso[:, 2:3]
# Plot the values
ax.scatter(x_vals, y_vals, z_vals, c = 'b', marker='o')
ax.set_xlabel('X-axis')
ax.set_ylabel('Y-axis')
ax.set_zlabel('Z-axis')
plt.show()
while X_iso is my 3-D array and for X_vals, Y_vals, Z_vals I copied/used 1 column/axis from that array and assigned to those variables/arrays respectively.