Manafort wasn't convicted "for state crimes."
First sentence of article: "sentenced earlier this year to nearly seven years in prison in connection with two federal cases"
And if you read the whole thing,
“Vance, a Democrat, said in March that a New York grand jury charged Manafort with 16 counts including residential mortgage fraud, falsifying business records and other charges. He said at the time that “no one is beyond the law in New York.” Manafort cannot be pardoned by President Trump for state crimes.”
He’s being held there pending trial on state charges. Rikers is not a Federal prison.