Regarding the whole Yankees/Mets/NYCFC thing, the big factor that everyone is missing in this conversation is that NYCFC had plans for a new stadium just south of Yankee Stadium, using a site currently occupied by an old parking garage and an elevator parts factory. In fact, it was their original idea, but for a long time it seemed like it couldn't happen because the team was unable to come to an agreement with the elevator parts company's owners about relocating the factory, so they explored other options around the five boroughs, only to eventually circle back to the original Bronx site when it seemed like a deal could be reached.
The city especially wanted to get that done because it would get that parking garage off their books. The city authority in charge of it is in the red because the building of the new Yankee Stadium included a couple of new garages closer to the new ballpark, plus the Metro-North railroad station built as part of it all means fewer people are driving to the stadium in the first place. And the capacity isn't as large as the old one. Essentially, there's now there's a relative glut of parking. The one old, further away garage was seen as expendable to everyone.
Except the Yankees. Who basically threatened to sue if the garage was totally removed as their deal with the city requires X number of parking spots within a certain radius, and the loss of the garage would drop the number below that threshold by like 800 spots. Despite the fact that even a sellout doesn't need those spots.
In other words, the Yankees torpedoed the deal that would have given the team that they partly own their own stadium. Around this time NYCFC also started having to deal with "scheduling conflicts" at Yankee Stadium that they didn't have before, resulting in them playing some home games at... CitiField.
It became completely apparent that the Yankees are not being good partners, so the NYCFC brass saw no issues with going to Willets Point.
Also, NYCFC was never about having a team necessarily in Queens or Brooklyn, just somewhere in the five boroughs (or really close) instead of in Jersey. As convenient as Red Bull Arena is to mass transit, just being on the other side of the river is a (frankly stupid) mental hurdle to some. Heck, remember that NYCFC was one of the groups that put in for what is now the site of USB Arena.