The Sears/Kmart parking lot site would destroy the customer base in Queens, and probably northern suburbs and LI, and maybe even the Bronx and Upper Manhattan. There are multiple close subways, but per google maps, my mass transit trip from a point in Queens less than 10 miles away would be about 90 minutes, roughly the same as going to RBA, because I still have to go to and through Manhattan, with at least one switch, to get there. I can't drive because it has no parking because you're building over the parking lot. I'm not riding bus and subways 3 hours (probably longer on weekends or late at night) for a soccer game.
The geography of NYC is unforgiving. Putting aside current uses and availability, if you don't want to exclude substantial parts of just the City itself, you're limited to Manhattan, maybe half of the Bronx, very NW Brooklyn, and very West Queens (including to a lesser extent parts of the 7 or E-F-R subway corridors). The same reasons those work are why they also are the most expensive and heavily developed locations with hardly any available open space.
You could put a Brooklyn specific USL club at the Sears location, just as QFC is building at a site useful pretty much only to Queens. But a MLS club for the entire city could not build in either location.