There's a lot about this plan that I don't like.
I can accept a charge to encourage long distance traffic to stay away from Manhattan, by charging more for driving within the perimeter, but there is a lot of this that does not seem at all fair.
The entire region's tolling structure must change in order for this to work. A fair system would be one where everyone driving to Manhattan will pay the same amount regardless of where they are coming from.
And AFAIK, the plan is to institute the charge both for entrance and exit from the charge zone (with special allowances for vehicles that will make multiple trips crossing the zone like taxis). With this being the case, all tolls in the region should be bi-directional.
Let's look at Hudson River crossings. Right now, Port Authority charges peak EZ-Pass $14.75, Tappan Zee charges non-NY $6.61, and NYSBA (Bear Mountain and other bridges north of Tappan Zee until just before Albany) charges $1.65. This does seem to correllate to charge more for crossings that are closer to the city, even though PANYNJ is way overboard given the pricing of the other crossings. Plus, currently there does not appear to be any discount or incentive within the PANYNJ crossings for avoiding Lower Manhattan.
So that these tolls correllate better with congestion charging, and given that all crossings are all-electronic-tolling, each crossing should charge half of their current amount, but in both directions.
A toll crossing to cross a body of water should be fully credited to the congestion charge. A toll crossing that simply moves people along quicker should not be credited, since there is a free option available. This means that if a driver crosses the Hudson and within 2 hours (before or after) crosses into Lower Manhattan, the congestion charge that is charged to the driver should be reduced by the amount of toll that the driver paid to PANYNJ, NYSBA, or Tappan Zee. But tolls on the Thruway (even in Westchester County) would not be credited.
The MTA toll crossings (except Henry Hudson) are $6.94 with NY EZ-Pass. This is the charge to cross between Queens and Bronx or between Brooklyn and Staten Island. The congestion charge to cross into Manhattan is likely higher, but the toll on any MTA crossing should be credited to the congestion charge. This means that a driver from Brooklyn to Manhattan will pay more than a driver from Brooklyn to Staten Island, but will be paying the exact same amount as a driver from NJ to Manhattan. And like he Hudson crossings, a toll can be credited to the congestion charge if made within 2 hours. So regardless if a driver drives into/out of Lower Manhattan on the Midtown Tunnel, Williamsburg Bridge, or Triboro Bridge (and then drives in south of 60th), the charge is the same. The toll on the Henry Hudson bridge, while lower than the other crossings, should also be creditable to the congestion charge.
West Side Highway and FDR drive should be free, in every sense of the word. In order to allow for this practically speaking, this means that travel on the Brooklyn Bridge to FDR should be free, the toll on the Battery Tunnel should be removed completely, and the congestion charging boundary should be moved to between 57th and 58th east of 3rd Ave. This would mean that the Queensboro Bridge touches Manhattan outside of the congestion zone, and regardless of using the lower or upper level of the bridge, there is free access to the Upper East Side via 1st and 2nd Avenues and also free access to the FDR (via 61st, 62nd, or 63rd).
What would all of this mean practically speaking?
NJ to Lower Manhattan. Since the price would be the same regardless, no one crossing would be favored. Each driver pays the congestion charge amount, and tolls are credited.
NJ to Upper Manhattan/Bronx/Westchester. The congestion charge would redirect drivers away from Lincoln and Holland Tunnels, and more would take GWB.
NJ to Brooklyn/Queens/LI. The congestion charge would redirect drivers away from Lincoln and Holland Tunnels, and more would take GWB or Staten Island crossings and then cross again with an East River crossing (Triboro, Whitestone, Throgs Neck) or Verrazanno. So each driver will face two tolls, but the price of the combination will always be the same, assuming they avoid Lower Manhattan local streets.
Bronx/Westchester to Manhattan. Free Harlem river bridges are preferred over Triboro or Henry Hudson because of tolling. However, if the ultimate destination is below 60th, there would be no preference in crossings, since the tolls would be credited to the congestion charge.
Upper Manhattan/Bronx/Westchester to Brooklyn/Queens/LI. The free option via FDR or West Side Highway will be available if using Battery Tunnel, Brooklyn Bridge, or Queensboro Bridge. The normal tolls apply if using Triboro, Whitestone, or Throgs Neck. Traveling through Lower Manhattan streets to make connections to FDR or West Side Highway will be most expensive and discouraged.
Lower Manhattan to Brooklyn/Queens/LI. Every driver will face the congestion charge once they reach or leave a local Manhattan street. The charge is exactly the same regardless of which crossing is used, whether you use a crossing that puts you directly in Lower Manhattan like Williamsburg Bridge, or whether you use a crossing that crosses outside the zone (like Queensboro or Triboro) and then cross into the zone, or whether you use the Brooklyn Bridge or Battery Tunnel to FDR or West Side Highway and then cross into the zone from the expressways.