"One of the things that Apple is priding itself in, is they're trying to get the best and the brightest," said Cramer, whose charitable trust owns shares of Apple and Facebook. "The best and the brightest that may feel Facebook is tainted."
Cook told Duke University graduates on Sunday that Apple takes a different path when it comes to data privacy, a possible jab at Facebook, which came under controversy over the use of its social media data.
Facebook drew criticism beginning in March over its privacy practices in the wake of revelations that Cambridge Analytica improperly gained access to data from some 87 million user profiles, then used it to target political ads. Cambridge Analytica denied any wrongdoing and has since gone out of business.
Despite the public uproar and slew of bad headlines, Facebook reported first-quarter profit and sales late last month that beat Wall Street's expectations.
It wasn't the first time Cook took aim at Facebook over its data leak scandal. Cook criticized the social media company during an interview in March with Recode's Kara Swisher and MSNBC's Chris Hayes, saying he "wouldn't be" in the situation Zuckerberg found himself in.
At the time, Cramer said Cook's comments showed that the "long knives" had been drawn for Facebook.
"Facebook, Alphabet – they're trying to get the smartest people," Cramer said on "Squawk on the Street" on Monday. "Apple wants the smartest people. IBM wants the smartest people. If you can say listen, 'We do not take your data.' They are going to be people that say, 'You know I feel much more comfortable going to Apple than I do Facebook.'"
Facebook did not immediately respond to CNBC's request for comment.