Methane, nitrogen, and neon wouldn't be too bad from a toxicity perspective, though neon would be expensive, and nitrogen isn't all that great in terms of density.

While methane is a greenhouse gas, as the article mentions, the amount used for balloons under any realistic scenario is going to be dwarfed by the megatons of methane that enter the atmosphere from natural processes (and, of course, natural gas is mostly methane). It's also dirt-cheap.