When I try to run app.py (Python 3.3, PyCrypto 2.6) my virtualenv keeps returning the error listed above. My import statement is just
from Crypto.Cipher import AES
I had the same problem (though on Linux). The solution was quite simple - add:
libraries: - name: pycrypto version: "2.6"
to my app.yaml file. Since this worked correctly in the past, I assume this is a new requirement.