The LIRR is over 100 years old.  It services the LI communities of about 3 million people to bring them into a city of 7 million.  The connection to Grand Central Station is needed to connect the largest commuter rail system in the country to the East side of Manhattan.  You try drilling 10 miles of tunnels under a river and through bedrock.  Let me know how it works out.  Oh, and all this construction had to be coordinated with Amtrak that owns the existing tracks under the East River and not be disruptive to existing LIRR, NJ Transit and Amtrak operations.

However, the lesson to be learned in all this is that estimates are never the final cost right up until the time of completion.  The current $10 billion estimate for our Rail is nothing more than a pipe dream given the fact that Rail is less than half complete with the most difficult construction yet to start.