U.S. Attorney Preet Bharara is making waves by taking on Albany's leadership, including possibly Senate Majority Leader Dean Skelos. However, a rebuke from a federal judge could affect the cases the prosecutor is building. Time Warner Cable News’ Zack Fink filed this report.

Once again, Preet Bharara is in the spotlight, with a high-level investigation of a public figure - this time, Republican Senate Majority leader Dean Skelos.

It has already been a big year for the U.S. Attorney, who in January indicted then-Assembly Speaker Sheldon Silver. But it was comments Bharara made just days after Silver was arrested that have raised eyebrows in the political world, with some accusing the U.S. Attorney of overreaching when he questioned the state budget process.

"The concept of three men in a room seems to have disappointingly taken root as opposed to being questioned. It's almost become part of the furniture," Bharara said back in January.

Last week, lawyers for Silver asked that the indictment be thrown out, saying Bharara has poisoned the potential jury pool with his comments. While allowing the case to move forward, a federal judge publicly admonished Bharara for his comments, saying the prosecutor was coming close to crossing the line.

"Prosecutors always have to be punctiliously factual about what they are doing and can't seem to be crusading in a way that is self-aggrandizing," said David Birdsell of Baruch College.

In a radio interview Friday, Former Governor David Paterson also questioned Bharara's tactics.

"You've got to be scrupulously careful not to go over that line where now he's talking about three men in a room and that kind of thing,” he said. “Now listen, they have three men in a room in Washington. You have three men in a room at every statehouse in the country. And they have three men in a room at the U.S. Attorney's office when they are deciding whether or not to indict someone. How about that?"

The Skelos investigation focuses on a business relationship with Skelos' adult son, Adam. This week, Silver's son-in-law was charged with running a Ponzi scheme in an apparently unrelated case.

"It's not as if we are talking about targeting minors. We are talking about people engaged in business relationships that may provide improper compensation to elected officials," said Birdsell.

At this point, there are no charges against Skelos, so it is premature to ask whether he would consider resigning from his position. It is worth noting however that the State Senate Deputy Majority Leader Tom Libous, Republican of Binghamton, is under indictment, and he has chosen not only to stay in his senate seat, but to also maintain his leadership position.