I've verified last year's AGI by ordering an IRS Transcript yet my return continues to be rejected. NYS does not allow paper filing. What should I do?

Did you try entering 0 for the AGI?  That works for most people.      If 0 doesn't work you will have to print and mail it.  It's ok to mail New York since you can't efile federal.  

Try using a Zero for your 2020 AGI.  There seems to be allot of returns that the IRS is rejecting for the AGI, the reason maybe because they were backlogged in 2020 & did not process returns until late.  So try using the Zero to see if your returns go through.