Were there more advantages or disadvantages to living in American cities in the nineteenth century?

A definitive answer to this question is, of course, not possible, because the question itself is quite subjective and would depend on the particular circumstances one takes into consideration, what social group they were focusing on, and what particular part of the nineteenth century they were referring to. We may consider here a few different examples to exemplify both the advantages and disadvantages of nineteenth-century urban life.
During the period of intensified American industry, the expansion of railroads, the increasing reliance on steamboats and steam-powered machinery, and the expansion of urban trade, which occurred from around 1810–1850 in the northeast and 1850–1900 further west, made life acceptable and, in some cases, quite enriching for certain sections of the population. Industrialists, factory owners, entrepreneurs, landowners, and market farmers all benefitted from the increased wealth that urban centralization and transcontinental interconnectivity produced. Urbanization also promoted the growth of a “middle-class” primarily made up of city vendors, merchants, office workers, writers, and other educated individuals who could make a good living through the many new occupations American cities had to offer. Even some subsections of the working class, especially union-laborers who worked in the coal mines, foundries, steel plants, or ironworks, could count on the continued demand for raw materials to provide them with a sense of economic stability (even though the nature of their work was often demanding and extremely dangerous). The American urban sprawl also saw the creation of standing municipal police and fire departments, professionalizing a line of work that was previously transitory and unreliable.
Unfortunately, as is always the case, urban life proved to be absolutely miserable for the poor. For example, after the conclusion of the Civil War in 1865, thousands of recently emancipated black men and women traveled en mass north and westward in order to create new lives for themselves in America’s burgeoning cities. This movement is known as the “Great Migration,” and it led to the immiseration of entire generations of black migrants. These newcomers were often forced to settle in the poorest neighborhoods in the city, which the municipal governments often refused to allocate money to or improve in any meaningful way. Furthermore, a large number of European immigrants, including the Irish, French, Dutch, and many peoples from Eastern Europe, began to settle in American megalopolises like New York and Chicago. Life for these immigrants was usually terrible, as they very often had little money, no social connectivity to their new host country, poor English, and few if any transferrable skills. The celebrated American author Upton Sinclair in his The Jungle provided an example of the difficulties faced by European immigrants to America (in his case, an immigrant from Latvia), and how these people were eventually denigrated to positions of abject poverty. Poverty, it should come as no surprise, was an inseparable part of nineteenth-century urban life.
Finally, a note may be taken on the state of technology and medicine during this period. Medical knowledge was still rudimentary, and most doctors still adhered to the miasmatic theory of disease, which posited that bad air was the cause of urban epidemic illness. Knowledge of microbes was still in its infancy, and, as a result, it was not unusual, for example, for poor parents to allow their children to drink fetid, cholera-infested still water from puddles in order to quench their thirst. Furthermore, industrial development is a dirty business, and the pollution generated from smokestacks, automobile use, and growing oil dependency made life in some parts of the city unbearable. Again, for the rich, who often lived in affluent neighborhoods far from the city’s industrial sectors, this was not a problem. But for the poor immigrant family, black resident, or even white day-laborer, these were constant threats.