The hacker Guccifer (Who alerted all to the situation by sending them the original emails) has said that he has saved all her emails to cloud and would give them to US authority at the appropriate time.
So it was a hacker who first alerted the government to the private server in her home.
Exactly.
The FBI interviewed Guccifer who is setting in a Romanian prison almost two years ago. My guess is they learned Hillary was using a private server at that time. If Guccifer got in, the NYT is shooting blanks.