According to News Radio in New York this am, the Secret Service will close down all trains to or through NYP during the time G. W. Bush is at the convention. No LIRR, Amtrak or NJT trains will operate during that time. No mention yet of the 7th or 8th Ave subways that bracket MSG.
Nothing final has been decided yet.
The Secret Service wants everything shut down, Amtrak, LIRR, NJT, and Subways. They apparently have gotten this type of cooperation in Boston for the Democratic Convention.
The NYPD is pushing for more security for Penn Station and maybe having Subways run by skip any stops near Penn.
If the Secret Service had its way, they would shut everything down every time the President moves anywhere. That is their job, protect him at all costs. However, in reality, they will have to work out a plan that satisfies the President (who may not want the bad press of forcing thousands of commuters onto busses), the NYPD, the NY Mayors office, etc etc.