What was bad about boss rule as practiced by machines like the Tammany Hall machine is that they were corrupt and sometimes violent.
The political machines made a practice of requiring bribes from various people, particularly those who wanted something from the city government. These bribes went partly to help immigrants and the poor (which was a good thing) and partly to enrich the leaders of the machines. The machines did give jobs and material help to immigrants and the poor, but they demanded that these people work on behalf of the machine, doing things like coercing people to vote in the "correct" way.
The machines were not all bad by any means. However, they were exceedingly corrupt and were concerned mainly with lining their pockets. These are very negative things.