Bronx is ideal. Its in some what would say New York City Proper. We know many in the boroughs refer to Manhattan as the City, there the stadium would be great. (I always pictured a stadium like Atletico;s vicente calderon in the city where the west side highway or FDR would go underneath one section of the stadium and the rest on the pier (
http://www.worldstadiums.com/stadium_pictures/europe/spain/madrid/madrid_vicente_calderon1.jpg)
But that seems far from happening, Manhattan, Bronx, Brooklyn, and Queens have so much waterfront for this (sorry staten island, you guys are cool you make it to Yankees and Mets game, but for the rest of folks Verazzano is too far, and majority of New Yorkers don't own cars or might get sick in the ferry)
Look at the Cosmo, they are out in Long Island, they can't even get a large fan base there. (South Bronx, is the closest space where negotiations are happening, and cheaper I think than either Queens or Brooklyn waterfront views) We know that Brooklyn waterfront will be hard, as you've noticed they even try putting a new apartments development with low income, and got rejected by community. Queens waterfront would be good, but LIC is getting pricier.
Randall's Island would be great, but lacks the necessary public transportation (subways).
NYCFC shouldn't share stadium with NYRB, even though its a nice stadium. The stadium's top priority should be that its built near public transportation (that spot in south bronx has 6 trains that go there (Eastside of Manhattan - 4 ,5, West Side 2, ,D, B and Metro North. Ideal for commuters.)
This new site in Queen's is inconvenient for us that only have one train to get there, and the idea of riding a bus to it is ridiculous as driving during rush hour there.