They have facilities that are used to keep "protected" inmates (ex. - informants, flippers) out of general population prisons that they could put him in and have him be the only inmate in the building.
When you get to this level of popularity, you get special rules. It's the same as how he just got endless warnings for breaking the numerous gag orders. They don't want to trigger a bunch of riots by his fan base, who would all be convinced that this whole thing is just political persecution.
His CFO is also doing his 2nd round at Rikers because he would rather purger himself then snitch on the crime boss. And also something to do with his "don't flip" NDA he has with Trump that gives him a bonus for not cooperating with law enforcement that came to light during this current trial.