My app is running on App Engine, but I would like to access its NDB DataStore entities from my Compute Engine VM to do some processing and write the results back to the App
David's solution requires you to use App Engine instance time to make requests, but you can bypass it and make requests directly to Datastore from Compute Engine instance. There is a pretty good tutorial about how to do this. But its not so pretty like ndb.
>>> import googledatastore as datastore
>>> datastore.set_options(dataset='project-id')
>>> req = datastore.BeginTransactionRequest()
>>> datastore.begin_transaction(req)