The mathematics of Gateway does not work if you try to finance if from user fees. Let's say that 100,000 people cross the Hudson one way by train now. We are including both NJT and Amtrak. If you charge them $1 for the tunnel, you get $200,000 a day because they go through there about twice a day. Being generous, I will give you 300 days in the year (not 365 to account for the weekends when commuter traffic is much much less). That totals $60,000,000 a year. In 30 years you will get $1,800,000,000. That is only $1.8 billion. You cannot wait for the money to pile up and then build Gateway, you need to borrow it in advance and pay it back with interest over those 30 years. Who knows what interest rates are going to be, but it is certainly fair to assume that you cannot borrow more than about half of your 30 year collections, or only $900,000,000. That is too little to build anything. So you need to charge more per person, say $6 one way instead of $1. Then you have a good amount of money to play with, $5.4 billion. Not enough to build the tunnels, but a meaningful amount.
Your problem is that that $6 just doubled the price of a lot of one-way commuter tickets, or at least added a very meaningful increase to them. What will happen is people will move to other modes of transportation. The tolls on the bridges and tunnels are charged only one way and are $15 for cash and $10.50/12.50 for EZ-Pass off-peak/peak. Even now buses are cheaper than the train, wait to see what happens if you add $6 to the price of all train tickets. NJT's ridership will crater. Amtrak's will be mostly OK, but you will still be left with less than half your original 100,000 riders and no way to get your $5.4 billion.
The only way to finance Gateway locally from user fees is to charge the same amount the non-Gateway users. That means everyone who rides the bus, and everyone who drives (twice if you collect the toll one way). In that case you might actually be able to get away with charging only $1 per crossing the Hudson per direction because now you are charging a lot more people (400,000+ per day per direction) and there will not be much transportation mode substitution. Good luck though convincing bus riders and drivers that they need to pay for Gateway -- infrastructure that they will never use themselves.