Having a game at Yankee is a novelty (see UConn/Army football); but, the stadium was not set-up for soccer (or any other sport). The sightlines for any sport except baseball at Yankee are poor and it is also too large (+40K) for a MLS stadium and too expensive for (parking, concessions, etc.) for families to attend regularly. The positive is that it is mass transit accessible; but, I do not know if Metro North will run trains for NYC FC games like they do for the Yankees.
Basically, Yankee Stadium has become the fall back location due to the original plan of building a soccer specific stadium in Queens near City Field being buried by local residents, a new Mayor, and the Mets. It would have been a good spot too as gave access to both NYC and Long Island, the later has been a strong soccer base for decades. NYC FC is even having problems creating a practice facility as local residents also shot down them building a facility to Manhattanville College that would have been used by both organizations.
http://www.empireofsoccer.com/training-facility-marketing-27691/