Trump announced on Thursday that he is nominating Jay Clayton, a former chairman of the Securities and Exchange Commission (SEC), as the District Attorney for the Southern District of New York.
"Jay is going to be a strong Fighter for the Truth as we, Make America Great Again," Trump said in a Truth Social post.
If confirmed by the Senate, Clayton will replace Damian Williams, who by tradition will submit his resignation when there is a change of President on January 21, or will be fired.
Last month, Williams filed the case against Vikash Yadav, a former Research and Analysis Wing (RAW) officer, alleging that he orchestrated a plot to hire a hitman to kill Khalistani leader Gurpatwant Singh Pannun.
Williams charged an Indian citizen, Nikhil Gupta, last year as a co-conspirator in the case.
He was extradited to the US in June from the Czech Republic, where he was arrested, and his case is proceeding separately at the Southern District of New York court.
Gupta has denied guilt in court and the next hearing is set for January 19.
Even if Williams quits, the lawyers in his office will continue the case until the new prosecutor and the new Attorney General decide on the next steps.
Trump has appointed a controversial former member of the House of Representatives, Matt Gaetz, as his Attorney General.
Yadav is described in the charges filed against him as a RAW "Senior Field Officer".
He is in India and is reportedly in custody facing kidnapping and extortion charges.
The Federal Bureau of Investigation has issued a "Wanted" poster for him.
He and Gupta are alleged to have tried to hire a person they thought was a professional criminal - but was a government agent - to kill Pannun.
The Southern District of New York covers Manhattan - and within it Wall Street - making the venue for most high-profile cases involving investments, and stock market trading manipulation and fraud.
As the former SEC head, Clayton brings special expertise to Wall Street and financial irregularities cases.
"He did an incredible job," at the SEC, Trump said.