From the few people I've spoken to with knowledge of the area, burying the tracks is a non starter. That spot is already prone to flooding from storms and burying the track would make it much more likely to happen unless the tunnel starts much further inland which would be immensely disruptive.
If the spot is prone to flooding wouldn't the tracks be useless? Would be an amazing spot if it could work. City should demand some major funds for cleanup and get it done.
Not saying the tracks aren't useless, but it's one thing to be on grade with 6" of water as the tracks can have drainage - it's another to have a tunnel under the water table with the 6" datum of water 10-20' above the tracks.
Ulrich is spot on with his assessment. At least, that's my understanding of it and I'm no engineer. 
As for them being useless. Kind of, they're very rarely used, and never for passenger travel. It's exclusively freight.
You also have to take into account how polluted the water table near the creek must be given that the creek is a Superfund site.
Jesus, I just realized the top three sites are:
1) A warehouse next to a toxic creek
2) A polluted piece of land occupied by repair shops for decades with no plumbing, next to another polluted bay.
3) The site of a parking garage and elevator manufacturing plant next to a highway.
None of these options scream "safe and healthy place to bring your family"
Well it is both. For maximum confusion we sometimes speak of them as if they are variations of a single site, and sometimes as separate sites. I'm certain many people are unaware there are actually 2 sites there close by.
It would, in theory. It would just be an added cost that constrains the size of the stadium they can build and if you're going to spend a few hundred million on a stadium you don't want it to have a weird angle. I mean, why leave one weird set up for another?
Not opposed to the plan if NYCFC can assist and leverage and simultaneously build a stadium on Willets West.
