i don't think putting another MLB team in the NY metro area would do much at all to damage the Yankees. They've got over a century worth of history and a massive fan base (both die-hard and bandwagon).
Plopping a brand new team down in Brooklyn would hardly put a dent in the Yankee machine. The area will still have the same amount of people (which means the same amount of households where the YES network is installed, and thats where all the $$ is coming from) and its not like millions of people are going to go from rooting for the Yankees to rooting for an expansion team. A team in CT makes even less sense (again, if your only objective is to hurt the Yankees) because you'd theoretically be pulling fans from the red sox as well.
A couple of things.* If you plopped an MLB team into Brooklyn in 2010, it wouldn't hurt the Yankees in 2011 but by 2015, 2020, you would see some shifted loyalties. Friends and I already were substituting going to Brooklyn Cyclones (Mets Class A affiliate) for going to see the Yankees or Mets. So another team would gradually, and ultimately, erode their leverage.
* Putting a team into CT: CT is basically divided, geographically, into Yankees and Red Sox camps. If you put the team more near NYC you'd disproportionately affect Yankees fans. But even if you drew off some Red Sox fans, I don't see that as a bad thing. Or you could choose some place in NJ. At the end of the day, the particulars aren't important just the idea that a lot of the Mets and Yankees revenue edge derive from their sharing of the New York market. The best way to dull that edge isn't to create something structural in the league that will be negotiated and loopholed around but rather a direct assault on the competitive advantage itself.