This is the area I was thinking of. Highlighted portion is 10 acres. Requires acquiring property but so will most locations. You're getting into 2 or 3 commercial parcels, from the satellite view. You could also backfill part of the creek which could reduce the need to acquire land.
As another option, if they can get cooperation from MTA (might require Amtrak as well), and can bear the additional building cost of going over the railyard, the previously mentioned Sunnyside yard idea is another good one. Remember building over a railyard was the original idea for the Jets West Side stadium as well.
That area you identified is extremely busy. I go into that little side street under the bridge monthly because a nano-brewery called Transmitter Brewing is located around the corner from the TNT USA marking on your map. Trucks come in and out of that cul-de-sac constantly. It is extremely heavily used. The parking spots under the bridge are filled weekdays and weekends. Point is, to get that land you would have to convince at least one and maybe more than one business that are heavily invested there to move. I don't see it happening.