If I can indulge into a quick foray into pop culture, one of the best songs in the musical 1776 is called "Molasses to Rum" and comes in the second act, as Jefferson's lines about slavery in The Constitution are being debated. I can't speak how it was staged when it was originally on Broadway, but in the current version, the performer playing South Carolina's John Rutledge uses the song as a way to embarrass the Massachusetts delegation. She leans heavily into the idea of hypocrisy and (to be sure, I was so impressed by her performance that I may be remembering it slightly differently than she played it) how effective New England had been at convincing the other colonies and themselves that their hands were clean.

Your question - and how you describe Tufts article (which I'm not familiar with) - speak to the effectiveness of that New England messaging. In affect, they affirm that the character of Rutledge correctly called out New England hypocrisy. And it's a fairly common worldview and it is possible that someone else can provide evidence from the historical record that race relations in the city in the 1800s were harmonious. I however, am going say that no, in the 1800s Black and white citizens of Boston did not peacefully co-exist and the lens I'm going to use is education.

Massachusetts - long before Horace Mann arrived on the scene - as a colony and then as a state saw the value of education for white children. By the 1800s, there were several schools for preparing boys for Harvard (known as Latin schools), a network of academies that provided a grammar school education to the children of merchants, and charity and state-funded schools for children whose parents could not afford to pay tuition. Despite town, county, and state legislation and policies using phrases such “schools for the instruction of children” and “for the benefit of all the inhabitants of the town" without specifying any class, color, race, or gender, these schools, were typically only accessible to white children, mostly boys. As slavery was outlawed across the region and free Black families built homes and communities in the state, they had to obtain tutors or set up their own schools as the adults who ran the white schools did not want Black children attending the school or Black parents did not want to send their child to school in a place where they would not be welcome.

The first known school created for the education of Black children in Boston was the "African School" established in 1798 by a formerly enslaved man named Primus Hall. Held in Hall's home, the school moved to the African Meeting House in the Baptist Church in 1806 and then was reformed and reestablished as the Abel Smith School in 1835. By that time, the school was no longer independent and had been subsumed by part of Boston General School Committee's efforts to bring all schools in the city under one umbrella. Before this point, Boston schools were informally segregated - Black parents saw to their own children's education, either at the Abel Smith School or via a tutor and white parents continued or as they had since the Revolution (tutors, academics, feeder schools, etc.) After that point though, Boston schools became formally, if not legally, segregated: the Committee built and oversaw schools for white children and schools for Black children.

This system didn't work from the beginning for the simple reason that the Black schools were under-resourced and poorly maintained. Many of the schools fell into disrepair and the Committee had little interest in ensuring the schools had the same level of resources as white schools. When the Abel Smith School fell into such a state of repair, parents feared for their children's safety, they organized petitions and appealed to the Committee for funding support. These petitions not only asked for better funding, they explicitly addressed the inequities and injustice of a segregated system. While these petitions didn't meaningfully change anything about how the Committee approached Black schools, they were the impetuous for a creation of a network Black parents, legal professionals, and religious leaders.

So, in 1847, when five-year-old Sarah Roberts her father were turned away from two white schools and told she had to attend a cold, run-down Black school farther from her home, her father had a network he could turn to in order to take legal action. Sarah Roberts v. City of Boston - more than a hundred years before Brown v Board - became the first legal effort to desegregate schools. Like Brown, the Roberts case focused on two main points: the injustice of segregation and that the system denied Black children the resources available to white students. Unlike, Brown however, the judge hearing the case ruled in favor of segregation.

The committee… have come to the conclusion, that the good of both classes of school will be best promoted, by maintaining the separate primary schools for colored and for white children, and we can perceive no ground to doubt, that this is the honest result of their experience and judgement

If this sentiment sounds familiar, it's the basis for the idea of "separate but equal" and the Roberts ruling was cited in the Plessy v. Ferguson ruling 50 years later. Schools remained segregated, Black schools receiving fewer resources than those attended by white students. All of this history happened before the New Deal and Redlining and played a pivotal role in the efforts to desegregate schools in the 1970s.

/u/Kochevnik81 has previously answered the very similar Boston was well known to be an abolitionist/anti-slavery city and was a popular destination for escaped slaves. By the mid-20th century the city had developed a reputation for being exceptionally racist. What exactly happened to cause such a drastic change in attitude?

More remains to be written.