The Russian anti-corruption activist was poisoned with Novichok nerve gas by Russian security forces and is now serving a three-year prison sentence, which he has protested with a hunger strike.
“This is the political persecution of a political enemy,” he said, before getting the Russian opposition leader’s name wrong.
“This is what Vladimir Putin does. Just ask Navatny.”
He then branded the charges brought by the Manhattan District Attorney’s office on Thursday as “banana republic stuff”.
Mr Weisselberg, who has worked for the Trump family since 1973, pleaded not guilty when arraigned on the 15-count indictment.
Prosecutors allege that the Trump Organization and Mr Weisselberg carried out a 15-year tax fraud scheme to funnel more than $1.7m in untaxed “indirect employee compensation” to the executive.
Mr Trump’s company is accused of failing to make US tax authorities aware of the payments.
“It was orchestrated by the most senior executives, who were financially benefiting themselves and the company, by getting secret pay raises at the expense of state and federal taxpayers,” Carey Dunne, an assistant district attorney, told the judge at the hearing.
Donald Trump Jr and Eric Trump, the former president’s second son, both helped run the company during their father’s time in the White House.
No charges have been brought against Mr Trump or any of his children, although the investigation is still underway.
Mr Trump has described it as a politically motivated “witch hunt” at a damaging his reputation and business.
Mr Weisselberg was released after surrendering his passport and is due back in court again in September.
German doctors concluded that Mr Navalny was likely poisoned after he fell ill on a flight from Siberia to Moscow, and he was eventually transferred out of the country for treatment.