Hunter's collections are no longer housed in one place. His library of books and manuscripts is now cared for by the University Library at Glasgow. A small number of his paintings ended up elsewhere, and there are other collections relating to Hunter's professional life and associates which may be of interest.
Glasgow University Library, Department of Special Collections - William's manuscripts and books
Hunterian Museum, Royal College of Surgeons, London (John Hunter's collection)
My Highest Pleasures - a 2007 exhibition catalogue documenting Hunter's art collections (available from GU online shop)