At which stage of enlightenment are the aggregates seen as not-self fully? In the Khemaka Sutta (https://suttacentral.net/sn22.89/en/sujato) Khemaka is an Anagami and he sees the aggregates as not-self. Based on this I guess the answer to my question is probably stream-entry or anagami, but I'm not sure.
This is a quote from that sutta:

“In the same way, reverends, I don’t say ‘I am’ with reference to
form, or apart from form. I don’t say ‘I am’ with reference to feeling
… perception … choices … consciousness, or apart from consciousness.
For when it comes to the five grasping aggregates I’m not rid of the
conceit ‘I am’. But I don’t regard anything as ‘I am this’.
Although a noble disciple has given up the five lower fetters, they
still have a lingering residue of the conceit ‘I am’, the desire ‘I
am’, and the underlying tendency ‘I am’ which has not been eradicated.
The conceit ‘I am’ is the 8th fetter; only fully eradicated by an Arahant.

Bhikkhus, there are these five higher fetters. What five? Lust for form, lust for the formless, conceit, restlessness, ignorance. SN 45.180

The stream-enterer has overcome 'identity view' ('sakkaya-ditthi'); which means seeing the group (body; kaya) of aggregates are not a self. However, the stream-enterer's seeing of the aggregates as not-self is obviously not complete enough to remove all ten fetters and uproot all outflows of defilements &amp; conceit.
Therefore, arahant is the stage of enlightenment where the aggregates are seen as not-self fully.