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
The officially recommended way is to use the datastore client libraries; see https://cloud.google.com/datastore/docs/reference/libraries You need to create a service account, or use the standard compute engine service account, give permission to either all APIs, or to datastore to that service account, and create the compute engine instance to be part of that service account. See here for more information. Then you can do something like:
from google.auth import compute_engine
from google.cloud import datastore
datastore_client = datastore.Client(project='yourproject',
credentials=compute_engine.Credentials())
q = datastore_client.query(kind='YourEntity')
q.add_filter('field_name', '=', 'HelloThere')
print list(q.fetch(1))