Reverend Al Sharpton delivered a powerful eulogy at Mount Neboh Baptist Church. Sharpton included remarks condemning vigilantism.
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Neely, 30, died after Marine Veteran Daniel Penny, 24, put him in a chokehold on an F train earlier this month.
Lawyers for Penny say Neely was threatening passengers, but a grand jury handed up an indictment and Penny has since been charged with manslaughter.
"We shouldn't not celebrate Jordan's life, but we should not forget how he died. We're not here because of natural causes," Sharpton said at the start of his eulogy. The reverend equated Neely's life of struggle to constantly being choked.
"A good Samaritan helps those in trouble, they don't choke them out," he added to much applause. The church was filled with mourners who often chanted "no justice, no peace" during the service.
"He was a homeless man but he was a human being. You don't deserve that. No, nobody deserves to die like that," mourner Noel McDonald said.
The former Michael Jackson impersonator more recently battled mental health problems and was in and out of psychiatric care more than 40 times, arrested another 40 times, and even accused of brutally beating a woman.
"Jordan was not annoying anyone on the train. Jordan was screaming for help. We keep criminalizing people with mental illness. They don't need abuse, they need help," Sharpton added.
Family members have said the trouble really started after Neely's mother was brutally murdered in 2007. The funeral for Jordan's mother was held at the same church.
In a new interview on "Nightline," one of Neely's aunts says he was homeless by choice.
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"So did anyone in the...Do you think in the immediate family had a sense of where his life was, where he was both physically and mentally in the last year or two of his life?" asked Byron Pitts, ABC News.
"Not to my knowledge," said Midlred E.J.B. Mahazu," Neely's aunt. "I wouldn't consider Jordan being homeless. Jordan just liked to be out. He had a grandma and a grandpa here. He had aunts. He had uncles, right here. He just didn't want to be tied up, I guess. He'd do what he wanted to do concerning that, so we couldn't make him."
"So he, his choice was to live on the street?" Pitts asked.
"I assume he did," Mahazu said.
Sharpton stressed that the Neely family should not have to stand alone as they grieve Jordan's loss.
"In your name, we're gonna change how they deal with the homeless. In your name, we're gonna change city services. Jordan, you didn't die for nothing," Sharpton said.
Sharpton thanked Congresswoman Alexandria Ocasio Cortez, who was at the service, for her advocacy for Jordan.
Eyewitness News learned detectives are still looking to interview people on that train, including at least one of the men who helped Penny hold Neely down.
There have been conflicting accounts from witnesses, some believing the chokehold went too far, while others are calling Penny a hero.
"If you look at Jordan, he was defenseless. He didn't fight them. He was just like, combo sweet. And I just feel bad for both families," mourner Sharon John said.
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The marine veteran is out on a $100,000 bond after being charged with second-degree manslaughter.
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