Any politician or bureaucrat who purports to know what is "going on" with the project is usually talking out of both sides of their mouth. Appropriations (which are usually the result of politics) are what determine funding levels.
The Transportation Bond Act has no funding for the TZ Bridge replacement on either side of the bond (MTA or NYS DOT). This makes sense when you consider that the study group hasn't figured out what they need, much less what they want. Unless you want study/feasability funding, it's hard to demand appropriations (from the bond act or anywhere else) unless you can quantify what it is that you're going to wind up with. "Earmarking" the funds at this point is just asking for them to be squandered on something else -- look at how much money has been set aside for the Second Avenue Subway project, going back to the 70s.
Speaking of the bond act, one of the biggest reasons it may fail is because the DOT has done a HORRIBLE job of promoting the non-MTA benefits. Half of the 2.9 billion in bonds they are looking to float is earmarked for transportation improvements around the state.
If you read the project lists (and I will provide both below), the worst project across both agencies has to be the 100 million for the downtown JFK link. Any real solution will involve 30-40 times that amount (to pay for new tunnels into Manhattan)
Back to the topic: The reason I listed the site was to show the official progress of the site, including all the rail options that may be included. The official press release and supporting documents provide details of interest to readers of this board that may be misinterpreted or not disclosed by journalists covering the story.
Since they are still in the enviornmental review phase (and the site makes it clear), discussions on funding are premature at best.
Nester
DOT Project List:
http://www.dot.state.ny.us/files/bond_act_alpha.pdf
MTA Project List:
http://www.mta.info/mta/bondact.htm