Sanders questioned whether Clinton's campaign violated legal limits on donations by paying her staffers with funds from a joint fundraising effort by Clinton and the Democratic National Committee, or DNC.
Sanders has long maintained that the DNC has favored Clinton over Sanders. The U.S. senator from Vermont is a democratic socialist who has run as an independent in his Senate campaigns.
“While the use of joint fundraising agreements has existed for some time - it is unprecedented for the DNC to allow a joint committee to be exploited to the benefit of one candidate in the midst of a contested nominating contest,” Sanders' campaign manager, Jeff Weaver, said.
The Clinton campaign dismissed the charge, with chairman Robby Mook saying Sanders was making baseless accusations.
"It is shameful that Senator Sanders has resorted to irresponsible and misleading attacks just to raise money for himself," Mook said.
The accusations surfaced as the Democratic and Republican candidates engaged in a final frenzy of campaigning before Tuesday's primaries.
Both the Democratic and Republican primaries are expected to be the state's most decisive in decades in the selection of the parties' candidates for November's general election.
Former U.S. Secretary of State Clinton and Republican Donald Trump, the national front-runners, were favored to win their respective primaries in the state that both call home. Victories would be a tonic for both candidates following a series of losses.
In recent weeks, Sanders has defeated Clinton in nominating contests. On the Republican side, U.S. Senator Ted Cruz of Texas, Trump's closest challenger, has outmaneuvered the billionaire businessman in the fight for delegates to the Republican National Convention that will pick the party's nominee in July.
By the end of Monday - the last official day of campaigning before the New York primaries - tens of thousands of New Yorkers will have heard the candidates' closing pitches.
At St. John's Riverside Hospital in Yonkers just north of New York City, Clinton spoke to doctors, nurses and others at a hospital cafeteria, asking for their votes and taking a jab at Cruz's dismissal earlier in the campaign of "New York values."
"I think New York's values are America's values," she told the crowd.
Cruz defended his "New York values" catchphrase on ABC's "Good Morning America" in Times Square on Monday, saying New Yorkers had "suffered under the left-wing Democratic policies" of New York City Mayor Bill de Blasio and Governor Andrew Cuomo.
Sanders needs a strong victory in New York, where 291 delegates to the Democratic convention in July are at stake, if he is to overtake Clinton.
With 2,383 delegates needed to secure the Democratic nomination, Clinton has 1,758 to Sanders' 1,076, according to an Associated Press tally. That total includes unpledged superdelegates who are free to back the candidate of their choice but told the news service whom they support.
For Trump, the question is whether he will make a clean sweep of all 95 Republican delegates at stake by earning the majority of votes in all 27 congressional districts in the state.
Total victory in New York would help Trump avoid the possibility that the nomination could be wrested from him at the party's July 18-21 convention in Cleveland if he arrives without a majority of at least 1,237 delegates. In that scenario, another candidate could win on a second or subsequent ballot.
Trump has 744 delegates to 559 for Cruz and 144 for Ohio Governor John Kasich, according to the Associated Press. The count includes endorsements from several delegates who are free to support the candidate of their choice.
In Wyoming, in the latest state-by-state delegate battle, Cruz was awarded all 14 delegates, according to a party official on Saturday.
"Lyin' Ted Cruz can't win with the voters so he has to sell himself to the bosses-I am millions of VOTES ahead! Hillary would destroy him & K," Trump tweeted on Monday.
On ABC, Cruz responded by saying that Trump was throwing a fit because he has lost several recent state contests.
"The stakes are too high to hand the election to Hillary Clinton, which is what nominating Donald Trump" would do, he said.