Until you can define what a thought is, you can't assert that it requires a functioning brain. Thoughts may well interact with the physical brain to produce measurable brain activity, but this in no way defines the origin or nature of thought.
Well, there is plenty of research in neuroscience on the relation between brain activity, and things such as memory, feelings, emotions, thinking, decisions, and so on. For example, some kinds of brain damage seem to show an impairment in these processes, e.g. loss of memory, difficulty in thinking, emotional disturbance. Are you saying that there is plenty of research into the non-material aspects of thinking? Citation?