I imagine checked bags will have to go to boston and then come back down the overnight regional to NYP, if GCT doesn't have the facilities...but that would be confusing if baggage is delivered other than to the ticketed terminus
There was a baggage car on the Shuttle 448/449 with luggage transferred from one train to another. There is not typically any other train with baggage service over the Empire Corridor although the connecting Empire Service train could temporarily run with a baggage car like the NER did for the Crescent last year. However, an area for checked bags would need to be set up at Grand Central.AFAIK, the only checked baggage between NY and Albany is the LSL. Boston passengers did across the platform transfer for an extended period while the work was done in Albany, I realize it involved less passengers, but the it wasn't too bad. How was baggage dealt with then?