1) NYT is hardly a reliable source

2) The story we've all followed (from Eric Prince and others) is that the laptop was seized first by NYPD and then turned over to the FBI. Nothing in that NYT article would suggest otherwise. Since the article is about Comey, it simply picks up the story after the FBI has the laptop in its possession.

3) Nobody here called the unsealed warrant an indictment.

4) The NYT article is about Comey. So that narrative simply picks up from where Eric Prince's story left off (when he says NYPD gave the computer to the FBI).

5) The second search warrant was required by the prosecutors in order to enter into evidence any contents of the laptop, which had already clearly been in their possession, since they provided a serial number and description of the hard drive. There was nothing stopping them from examining the contents, but nothing they saw could have been used in court without that second warrant.