Assuming you imported matplotlib.pyplot as plt, try plt.ion() at the start of your code. This enables interactive plotting. If this does not work, you may need to change your backend, See the matplotlib FAQ for details on this question.
There are a couple of Python modules that will let you do this, I would suggest using sounddevice. It can be installed with pip or conda: python-sounddevice as is built on top of the platform independent PortIO package. The documentation has lots of examples, ranging from very simple to sophisticated.
The soundfile module is a Python interface to an established cross-platform open source library, libsndfile, that can read a variety of different audio file formats. Install pysoundfile with pip or anaconda, and see the documentation for examples.
Go to File->Settings then select Python Scientific in the settings box. Uncheck “Show plots in tool window”.