You can use C_NewItems to query whether an item is new or not, then clear it manually.
Lua Code:
isNewItem = C_NewItems.IsNewItem(bag, slot)
C_NewItems.RemoveNewItem(bag, slot)
C_NewItems.ClearAll()
Note that in the case of stacks, your stack will not be flagged as new when you loot another item of that type.
The default UI uses this class to highlight new items in your bags, and it also clears all new items whenever you close the container they're in. You'll have to do the lookup on BAG_UPDATE and clear them yourself before the container frame gets a chance to do it. This way you can track any new item that you acquire.