Wherever the Torah refers to thinking and feelings of Anger, compassion etc. it always mentions the Heart as the controlling organ (also Kidney) but NEVER the Brain? (Even in the G'mara the Moach is rarely mentioned).
The word מוח only turns up once in Tanakh anyway (Job 21:24). It means "marrow". Onkelos translates קדקוד in Deut 28:35 as מוח, and we see it with a similar meaning ("brain", and the membrane around the brain) in the early rabbinic literature. The fact that it's not mentioned in the Tanakh can be due to their either having a different word for the same thing, or to the fact that it's a part of the body that they never speak about. Either way, they did not consider it the seat of thought.
The first person in recorded history to recognise the brain as the source of thought and understanding was Alcmaeon of Croton, a Greek philosopher and physician who lived in the 5th century BCE.
the vilna gaon on yona says: http://www.dafyomireview.com/yonah.php
(1:5 And the sailors were afraid, and cried out every man unto his G-d; and they cast forth the wares that were in the ship into the sea, to lighten it unto them. And Yonah went down into the depths of the ship; and he lay, and was fast asleep. )
VILNA GAON: And the sailors were afraid - They are the leaders of the body, which is the brain, heart, and the other powers.
LATER ON HE ADDS 1:6 So the shipmaster came to him, and said unto him: 'Why are you sleeping? arise, call upon your G-d, if so be that G-d will think upon us, that we perish not.'
VILNA GAON:So the shipmaster came to him He is the head leader (of the body) - the heart.
LATER ON 4:11 VILNA GAON: That the two inclinations which advise for the good or for evil, as it says (Kohelet 10:2) "the heart of a wise man is in his right, while the heart of a fool to his left". But the tzadik serves G-d with both, as written "with all your hearts" (Devarim 6:6) which means with both your inclinations, END So it seems thought can arise in the mind but the heart is the one who decides/rules what to do therefore it is considered the real thinker