Yes, think that humans tend to think with more than just their brain at times. Emotions and other things come into play when some decisions are made. Pain is another issue that may alter someone's thinking. So in the end it takes more than just the brain for a person to think.
I definitely think that humans think with their entire bodies. While of course its silly to not realize the brain is the part of the body responsible for all our thoughts and actions, I think that the whole body is a living organism that the brain cannot live without. It is important that they all work together to process a thought.
We may like to believe that we "think" with our stomachs when we are hungry, or our hearts when we feel love. But the truth is that it is the brain and the brain only that analyzes situations and makes decisions. Hunger, for example, is merely a message from the stomach to the brain that it needs nourishment, but it is the brain, in this case and all other cases, that makes the decisions to act (or not act) based on those signals.
What would define "thinking" in this situation? Receiving information or processing it? In order for a brain to properly work, it needs access to information. This information can be obtained from sight, sound, touch, smell, or taste (maybe a third eye if you believe in that sort of thing). That is all RECEIVING information though. The brain is what does the actual processing. It is what takes the sight of a stop sign and alerts the rest of the body to stop. The rest of the body is replaceable as far as information input is concerned. If you don't have sight, your hearing and smell gets better. If you don't have hearing, you pick up on more visual cues. On the opposite side, if you don't have a brain, you are unable to function.
It is only the brain in the human body that can think. If you need proof of this look at any person who is brain dead, the rest of their body stops working. The brain is the only part of the human body that is capable of thinking in any capacity.
The body is just connected to the brain and that is why it feels like some body parts have a mind of their own. The brain can sometimes send strong signals to other body parts. The body also can put off certain chemicals and it makes you brain react differently.