Is it possible to have multiple PyPlot windows? Or am I limited to subplots?

Sure, just open a new figure:

import matplotlib.pyplot as plt

plt.plot(range(10))

plt.figure()
plt.plot(range(10), 'ro-')

plt.figure(), plt.plot(...)

plt.show() # only do this once, at the end

If you’re running this in the default python interpreter, this won’t work, as each figure needs to enter the gui’s mainloop. If you want to run things in an interactive shell, look into IPython. If you just run this normally (i.e. put it into a file and call python filename.py) it will work fine, though.