Very difficult.
I will have to do it by regions:
Of the Western Isles, I loved Barra most with Eriskay a close runner-up. However, Lewis (especially the west coast around Aird Uig) and Harris with its beaches are great as well.
Of the Inner Hebrides it is a draw between Islay and Jura (can not decide which I love more)
Of the North Isles, I would say Unst so far but I plan to re-visit Shetland soon so maybe I will find a new favourite then
A compeletely underrated set of islands, by the way, are the Slate Islands. I've been to Ellenabeich (Seil) and Easdale - beautiful!
But of course the absolute queen of all islands is St. Kilda....