I was thinking, what about the area around 149th street/ grand concourse?
http://mapfrappe.com/?show=46258
Most of whats there is either somewhat run down brownstones, somewhat run down industrial or other things that can be worked around. The only decently sized hiccup would be the Bronx terminal market. You don't even really need to get into rerouting or otherwise making grand concourse subterranean.
You get to use all of the Yankee stadium parking as part of your plan, and your actually equidistant from the metro north stop compared to Yankee stadium. And the 149th st station is right there.
Better yet, you can fit a full metlife part 2 electric bogaloo on that space, with some spare area for a stadium entrance park.
Idk man, these guys might think they own the place if we build on top of them: