Town of Hempstead Supervisor Don Clavin and the Town Board presented the award to the 17-year-old from Garden City, who is blind, to celebrate her outstanding achievements.
A special plaque also included a message in Braille.
"Just the fact they are putting accessibility into the world, because not a lot of things are set up for me, so just having that is so special," Pagonis said.
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Pagonis also competed in the women's 200-meter individual medley, where she set an American record and won a bronze medal.
"I was beside myself," her swim coach, Marc Danin of Islander Aquatics, said after her win. "My heart rate was over 120."
Because of COVID-19 safety protocols, he couldn't travel with her to Japan, but he was coaching from afar and knew she'd prevail.
"I said from the beginning, when she said that this was her goal, I told her, 'You're going to win the gold,'" Danin said.
Pagonis started swimming when she began to lose her vision as a 12-year-old due to a genetic retina disorder called of Stargardt's disease.
She admits that she was very depressed when she was diagnosed, suffering from thoughts of suicide. She also stopped eating and retreated from family and friends.
"I felt worthless and hopeless," she said. "And if I was going to be blind, then what was the point of me living?"
Family, friends, and doctors helped Pagonis cope with her visual impairment, but at the end of the day, her own will to live her best life helped her most.
"The support from them really helped me, but if you are coming out of a dark place, I think it comes from you," she said. "Obviously, all these things help you, but it really comes from you.
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She is now a role model for children across the nation and a popular social media influencer on TikTok, with over two million followers.
"I grew up getting bullied a lot for losing my vision so I kind of made my social media my friend group if that makes sense," Pagonis said. "I'm just really excited to show people, even if you have a disability and some things go wrong, you can still pull through and there's light at the end of the tunnel."
Her goal is use the platform to raise awareness.
"Just showing everybody, 'Hey, this is what blind is, what blind looks like, and this is the things I can do being blind,'" she said. "My goal with social media is to show people that this is blind. I am not the stereotype of blindness. I want to show people that, yes, I'm blind, but I'm still going to wear makeup. I'm still going to dress the way I want to, and I still know trends because I have friends that can teach me. And I can be a professional athlete."
Her next goal is another shot at gold in Paris 2024.
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