I have good news to share.  With the recent release of NY to allow efiling, functionality on the CT-3-S has been added to allow users to enter the total PTET taxable income and credit on the CT-34-SH, pg 1 -3 form.  Scroll to the bottom and there is a worksheet that allows input of the PTET information.  

These inputs will be allocated prorata to the shareholders as required for s corporations as part of the supplemental statement on each K-1.  

Hopefully this will reduce the pain point requiring users to input the amounts for each shareholder.  Thanks to everyone for their input.