One difference that comes to mind is that the negative income tax requires all of the government machinery of the income tax to operate. If you decide to abolish income taxes in favor of something else, like sales or property taxes, you'd still need income reporting to compute everyone's benefit. A universal basic income is much simpler to operate because it's the same amount per-head.

If we're going to stay on an income tax system, then the negative income tax is probably smarter.

Interesting aside: Milton Friedman was a proponent of a negative income tax.