Instinct is a gut level "this is wrong" or "this is the right way to go". It's getting as much information you can about the decision in front of you, synthesizing it all and going with your gut.

Emotion is the "Oh Crap!" the "This rocks! I'm going to be a guhzillionaire." or "I'm doomed" feelings. Emotion is the "But I've worked so hard on this, I cant let it go" feelings.