"The eyes are the windows of the soul" is one of those quotations that never were, just as "Water, water everywhere and not a drop to drink" is...or "A picture is worth a thousand words". That is, nobody ever actually expressed the thought in exactly these words except by mistake! Consider, however...
a. "These lovely lamps, these windows of the soul" which is a quote referring to eyes from a work by Guillaume de Salluste du Bartas (1544 - 1590) called �Divine Weeks and Works'.
b. "Thou turn'st mine eyes into my very soul", are words spoken by Hamlet's mother in the play by Shakespeare (1564 - 1616).
c. "Eyes so transparent that through them one sees the soul" which is from a work by Theophile Gautier (1811 - 1872) called �The Two Beautiful Eyes'.
The lazily misquoted version that most of us use nowadays is just a corruption of one or another of these.