The way the MTA was created was because originally each line and the busses and all that were managed by different entities. They were consolidated over time to create one unified transit agency. Theoretically you could break them up and you could have the city take over the subway. Technically NYC owns the tracks the MTA just rents them for nothing. So its possible.

Only questions are how to do that and not cut service. Once people give up on transit it’s hard to get them back.