I think that it's in the administration's (and the feds') best interest to have crime organized. That way they're able to control it much more effectively.
If there was no more CN in NYC overnight then what? You'd have every man for himself, you'd have chaos, no order. So it's in their interest to have major crime as organized as possible, but of course, keeping it weak and not interfering with the general public. The CN is perfect in that way. Not to mention that now there are informants pretty much in every family so it's a lot easier to learn things also.
Bottom line, the only reason the CN is still alive is because they're useful... to the feds, to the government, even if some of them don't know it.