* I think prosecuting tax evasion is one reason. It's hotel tax actually and not income tax, but tax evasion is tax evasion. However, I don't see why AirBnB host should play by different rules than a b&b-style guest house.
* Same applies for zoning restrictions. We can debate if the current restrictions are sensible or not, but that's the playground and the rules and we all play by the same rules.
* Hotels are cesspools. Yes, some are. Even chain hotels are. I don't know about NY hotels but I've seen quite a few and they range from "great in all regards" to "glad I'm far away". All in all most hove been acceptable. B&B rentals are on the same scale. At least with hotels there's a place I can report violations to.
I fail to see any reason or moral right that AirBnB host should not have to register as a B&B place, not pay the applicable fees and not adhere to the applicable rules. They're totally free to do that and then advertise on AirBnB. However, the implied reason a lot of hosts don't do that is because their landlord won't allow them to sublet the apartment - but that's a totally different problem. I fail to see any moral right that your landlord has to allow sublets. It's also none of the states business.
There's a lot wrong with governments and corruption and often they're incompetent and played by interested parties, but I think it's wrong to always assume that as the primary cause for government action.