There seems to be a desire among even top researchers in economics to conflate the two; but I don't know how well founded or established the connection is.
It might be helpful to define intuition for this purpose. I think of intuition as a sense of reason to do something, without the rationale for that reason being clearly articulated in one's consciousness. A "gut" feeling might be intuition. And emotions are certainly "felt". For a functional perspective of emotions (as "recalibrational") that is also very "hedonic" or linked to feelings, check out this chapter which is soon to be out in a book:
2013. Schniter, E., Shields, T. Recalibrational emotions and the regulation of trust-based behaviors. In Psychology of Trust: New Research. D. Gefen (ed.), New York: Nova Science Publishers.
I'd have to agree with Eric's initial sentiments here - the core problem lies in defining and operationalizing intuition. Certainly, evidence from behavioral economics tends to suggest a key distinction between cognitive and affective processing modes where "better" decisions are typically found with cognitive bases but only for relatively simple tasks. Where tasks become complex, emotions-based reasoning appears to be more useful. Whether either of these could be considered intuitive I am unsure and it is certainly true that emotional and intuitive are treated synonymously by many.