Of course the Democratic Party is not a labour party. Still, there's a difference between a candidate being the lukewarm favourite of unions and unions regarding a candidate as their enemy. At least in principle.
A few unions consider Cuomo the enemy, but not all of the NY ones, trust me. The first step in winning political victories is dividing the opposition, and Cuomo's no stranger to that concept.
And this is 2011, Cuomo has a few years before 2016 when the budget situations won't be catastrophic and increased revenues (and public union expenditures) will be present.
I doubt Cuomo would run in 2016 and the anti-union candidate. He'd try and paint himself as pragmatic most likely for his brand, but present himself as pro-business to donors, I think. And five years is a long time, even if he wanted to change his brand.