I don't really think it's likely, but in no way is it impossible. After all Cheney had been, House Reprasentitive, Chief of Staff, and Secretary of Defense, before becoming VP.
Of course Emanuel would need to be promoted. He'd not be very successful running as Obama's CoS. However CoS rarely (never) serves for all the eight years, and neither does the secretaries in the cabinet. So if Emanuel can get himself promoted to a cabinet possition, where he does a great job and creates an imidge for himself, I could see it happen.
I'd much rather see your suggested ticket reversed though, Gillibrand/Emanuel in 2016
