If you set the D90's popup flash to commander mode and its power level to "--" it will fire a tiny burst of light just enough to trigger the Nissin, but not enough to contribute any meaningful light of its own. This is really only problematic with reflective surfaces because that pulse of light will show up, even if it doesn't affect the exposure in a measurable way.

Alternatively, Nikon makes an accessory that fits into the hotshoe and covers the popup, blocking visible light but allowing the IR signal to pass.