New Yorkers are eligible for a Fair Fares discount if their household makes no more than 150% of the federal poverty line — or $22,600 a year for a single person. The CBC argued that raising the threshold to 250% of the poverty line, or $39,900 for a one-person household, would do more to help the poor than making the buses free. The nonprofit estimated increasing the income limit would cost taxpayers $232 million a year, up from the $86 million the program currently spends annually.

Means testing is how you create programs that are doomed to fail from the start. Wealthy and middle class voters always start to resent the poors getting “free stuff” so programs get cut back until they buckle, and then they get eliminated. There is a reason the Republicans haven’t been able to destroy Obamacare, but not Medicare or SS.
Means testing also rarely saves the government money. All the extra bureaucracy for tracking eligibility usually costs more than it saves. It’s better to provide for everyone then make it up with progressive taxation.
The report’s argument is that making more people eligible for the existing means-testing while still making the rich pay (those making 400% of the US poverty level currently ride the subway as much as those 0–150%!) has been calculated to be one-third the cost of free busses. The program isn’t adding or restricting means-testing, which is what gradually happened to ACA Medicaid as you mentioned, but relaxing means-testing that already exists.
My argument against the report is that free fares would increase the bus ridership especially for the poor, invalidating the reasoning that it “wouldn’t reduce the costs of travel for most riders, since 76% of daily transit trips are on the subway”.