There were a few stories on this about a month ago or so, so some of them have probably dropped off the radar screens by now.
The bottom line last I heard was that Sheldon Silver was opposing the project, largely because he's under pressure from the Dolan family who own Madison Square Garden. They want the deal to be stalled until a larger deal that includes building a new MSG can be approved. They of course want this, because if they can't get included in this deal, then they will either have to spend millions on renovating the current MSG or building a new one with thier own monies. If they can get into the Moynihan deal, then they'll get some really nice tax breaks and at least part of the new arena will end up getting built with public money, instead of their money.
One story on this from the NY Observer is still available
here.
And another from NY Metro can be found
here.
Of course this project also has nothing to do with Amtrak anymore, even if it does go ahead. If this ever happens, Moynihan will only serve New Jersey Transit. And that fact IMHO, means that this project really should be cancelled. NJT can't afford to run yet another NY station, this will make 3 once The Tunnel is built. Moynihan is too far away from the 7th Ave Subway and the 6th Ave Subway for commuters and commuters don't really hang around the station for very long anyhow, so they certainly don't need a huge luxurious station.
Moynihan made sense for Amtrak customers who spend longer times waiting for trains, even though it didn't make sense for Amtrak to pay rent over there when they have the current station rent free. But it does not make sense for NJT.