No that was not the Hudson river leaking into the tunnel, but it gave a nightmare to the people who sat in their cars and watched the water overflow. The man who filmed the video, Anthony Consiglio also clarified that is was not the river but made people had Goosebumps for a second. The officials cleared that it was a leak in the central valve system that ruptured and caused the leak and was repaired as they got the information about the same.
The Lincoln Tunnel is an 80-year-old tunnel that carries millions of people in and out for New York. On further investigation with the port authorities of New Jersey and New York, it is clarified that there is nothing and the leak has been sealed and repaired.
Also, the water has been pumped out from the one and a half-mile long tunnel the commuters have started using it again as they did without any hassles. The people who watched the video were scared of getting stuck in the flooding tunnel but the situation was taken under control and pacified.