Before I start, I want to state that I am a newbie who knows nothing. I am hear to learn, so please bash me in positive way.
Staying at the level of the East Side Access tunnel, can Grand Central Station be connected with NY Penn Station? The ESA tunnel would continue under Park Ave until NYP East tunnels, where they would turn west to NYP under those existing tunnels. The idea would be to make the ESA to GCS a shared stop for both LIRR & MNRR which would then continue to a new level at NYP. The 3rd rail differences between LIRR & MNRR would need to be resolved with standardization - should be done regardless for two MTA branches. On ths board I have read that NJT wants to add new tunnels under Hudson River to new terminal near NYP and this connecting tunnel and new level under NYP could allow them access to GSC and still use SunnySide yards. This would spread the cost among at least 3 agencies, maybe 4 if Amtrak interested in NYP to CGS connection.
Another idea: At least one of the tunnels to this new NYP level should be made big enough for freight service between NJ & LI - another tunnel under East River to Main Line or LIC terminal.