I'm getting an input overflow error using pyaudio with sample rate of 16000 and frame per buffer of 1024. I'm also using a USB microphone and a raspberry pi 3 (raspbian). I'm using pyaudio for pocketsphinx and it works fine but stops with input overflow after a few seconds.

 p = pyaudio.PyAudio()
   stream = p.open(format=pyaudio.paInt16,
   channels=1, rate=16000, input=True,
   frames_per_buffer=1024,
   input_device_index=3)
   stream.start_stream()

I had the same issue and it seems to be due to an overflow of the buffer. Try increasing the size of the buffer to 2*1024 or 4*1024. I hope this helped

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