The whole situation seems quite chaotic for me, as I've read here in the comments. Different tolls on different tunnels/roads, different transit providers etc. It seems suboptimal.
I wonder why this is not better designed? At least the public transit situation can be improved, I think. While public transit in germany is quite complicated, I think it stems from a similar federalistic design and maybe the solutions can be translated?
We usually have local public transit owned on the local level, with regional rail owned by the state or the federal railroad company. So different actors like MTA or NJ transit, as I've understood (are there more?).
But we usually have another layer, a transport association. For example in munich it's the mvv, which is owned by the state of bavaria, the city of munich and the neighbouring districts, or the VBB in Berlin, owned by the state of Berlin, the neighbouring state of brandenburg and the districts of berlin and neighbouring of berlin in brandenburg. The transport association usually doesn't own tracks or rail cars, but it's responsible for uniform pricing, ticketing, coordinating schedules and distributing the money to the actual transit providers, which can be federal, local or the state (or multiple states as with berlin).
It is quite complicated and usually in germany nobody knows the difference between the transit providers and the transit association etc., but maybe this system can be translated? It usually leads to a situation where the transport association is perceived as a uniform system and hides the federalists structure behind a common front, and also as a common actor and formal way to coordinate on the future of the system between the different actors.