Yes. Ego and all other defilements are in vinnana.
However, we need to differentiate between vipaka vinnana and kamma vinnana.
– We experience the world with Vipaka vinnana. They are of six types: Cakkhu, sota, ghana, jivha, kaya, and mano vinnana. Even an Arahant experiences the world and has those vinnana.
– A kamma vinnana is a mano vinnana that arises via “avijja paccaya sankhara” and “sankhara paccaya vinnana.”
That kamma vinnana is purified as one cultivates the Path.
– Lobha, dosa, moha are gradually removed as one cultivates Panna (wisdom). Dasa samyojana (including sakkaya ditthi, mana, etc) are removed with stages of magga phala. All those can ONLY be removed via Panna.
– However, moral conduct (sila) is NECESSARY to be able to comprehend the Noble Truths and to cultivate Panna.
Thus, an Arahant WILL NOT generate kamma vinnana via “avijja paccaya sankhara.” But he/she would still have the vipaka vinnana, i.e., is able to see, hear, taste, smell, touch, and think.