Convert django RawQuerySet to Queryset

You can use a RawSQL expression:

ModelB.objects.filter(id__in=RawSQL(
    'SELECT unnest(a.pk_values) FROM app_modela a WHERE a.id = %s',
    [index_id]
))

Alternatively you can reproduce the exact query you have in your question with extra():

ModelB.objects.extra(
    tables=['foo_modela'],
    where=[
        '"app_modelb"."id" = ANY("app_modela"."pk_values")',
        '"app_modela"."id" = %s',
    ],
    params=[index_id],
)

Update: I got something working using .extra()

class CustomManager(manager.Manager):
    def get_for_index(self, index_id):
        qs = self.get_queryset()
        sql = "myapp_model_b.id IN (SELECT UNNEST(myapp_model_a.pk_values) FROM myapp_model_a WHERE myapp_model_a.id='%s')" % index_id
        return qs.extra(where=[sql])

Docs: https://docs.djangoproject.com/en/2.0/ref/models/querysets/#django.db.models.query.QuerySet.extra