This piqued my interest, so I checked: Tunnel #3 passes under the Harlem River and then the East River, but the Harlem River is less than 30 feet deep for the most part and the East River is around 40 feet deep at the most.

(The Army Corps of Engineers has great detailed depth surveys for most of NY's waterways[1].)

Edit: There's also a higher-resolution render of the tunnel layout here[2].

[1]: https://www.nan.usace.army.mil/Missions/Navigation/Controlli...

[2]: https://extapps.dec.ny.gov/docs/water_pdf/nycsystem.pdf