thoughts are electrical , emotions are chemical. Thoughts just pass by, come and go. But emotion have a longer curve, it takes a longer time to wear off, body has to process the chemical that is generated.
Thoughts are like driving a car  and emotions are like steering a boat may be.. with more inertia.
Thoughts are just in the head, emotions are felt all over the body,like tear glands and stuff :P. Its not just electrical signals, its chemical signals right? - serotonin and stuff like that. I havent gone into the biology of it.

why all this? why because..some times a bad thought comes creates some emotions, u have control over thought, u think of other things or u reason out with the thought but u cant expect change in emotion immediately.. u have to wait out for the emotion to be processed.

( In occult they talk of mental body being more subtle than the emotional body. Is this what they mean? Could be the "body" they talk about is just a representation or a model to make us understand the concept and not actual body around us? Just like sine wave is not really that curve we see but its a way of showing us how things change in time..)