You can use the set_label_coords method.
import matplotlib.pylab as plt
import random
import matplotlib.gridspec as gridspec
random.seed(20)
data1 = [random.random() for i in range(10)]
data2 = [random.random()*1000 for i in range(10)]
gs = gridspec.GridSpec(2,1)
fig = plt.figure()
ax = fig.add_subplot(gs[0])
ax.plot(data1)
ax.set_ylabel(r'Label One', size =16)
ax.get_yaxis().set_label_coords(-0.1,0.5)
ax = fig.add_subplot(gs[1])
ax.plot(data2)
ax.set_ylabel(r'Label Two', size =16)
ax.get_yaxis().set_label_coords(-0.1,0.5)
