State officials will also ramp up efforts to penalize retailers who sell tobacco and e-cigarettes to minors.
According to data from the New York State Department of Health, nearly 40% of 12th grade high school seniors and 27% of high school students overall "are not using e-cigarettes," according to a press release.
In a press conference on Sunday, Cuomo blamed the 160% increase from 2014 on flavors such as bubble gum, cotton candy and "Captain Crunch" that are "obviously targeted to young people."
"New York is confronting this crisis head-on and today we are taking another nation-leading step to combat a public health emergency," Cuomo said in a statement. "Manufacturers of fruit and candy-flavored e-cigarettes are intentionally and recklessly targeting young people, and today we're taking action to put an end to it."
E-cigarette flavors such as menthol and tobacco will not be banned based on recommendations from New York Health Commissioner Howard Zucker, as cigarette smokers often rely on e-cigarettes to wean off cigarettes when "nothing else" has worked, Cuomo said.
However, "that could change in the future," Cuomo added.
On Thursday, Cuomo signed an executive order directing state agencies to deploy education awareness programs on vaping, which will then be implemented into school systems, according to the release.
The state of New York will also raise the legal age to purchase tobacco to 21 beginning Nov. 13.