Joekinde, the existing Penn Station will continue to function.
The "New Penn Station" is really a dramatic above-ground expansion of the existing station. The current underground station runs from Seventh to Ninth Avenues. The expanded station will have a similar footprint, but will have two dramatic above ground spaces: the Moynihan (post office) portion to the west and the Penn Plaza (current MSG) portion to the east.
Therefore, there will be no loss of subway accessibility.
The NJ Transit expansion in the current station is separate from and compatible with the above-ground expansion.
The LIRR is not leaving Penn. They are just adding service to Grand Central. Similarly, there are plans for Metro North at Penn.
In addition to the planned NJ Transit expansion projects in the existing Penn, there will eventually be a large new station expansion underneath 34th Street. It will serve dramatically expanded NJ Transit routes once the new tunnel opens. This station will be connected to Penn and will serve both the existing tunnel and the new tunnel.