Dragon Magazine, issue 354, April 2007, with a Modron on the cover. Class Acts: Adventurer on pages 86 and 87 has Elements of Surprise, alternate class features for the Ninja.
The defaults of Ghost Step and Ghost Strike, along with the improvement to Ghost Step at 10th-level, are described there as traits of ninja drawing on the element of wind/air. Blinding Flash is described there for ninja drawing on the element of fire, blinding enemies with light instead of turning invisible. Deceptive Mist is for ninja drawing on the element of water, creating small fog banks that conceal their activities but without affecting their own vision. One with the Earth is for ninja tapping into the element of earth, melding into earth and stone to hide and travel through it. Naturally, they get improvements/additions to these capabilities as they advance in level, just as a typical wind ninja gets improvements for use with Ghost Step.
I can't remember now if there was another Class Acts article with alternate class features for ninja, only one or two for feats and items that I can recall. Page 87 in Dragon 351, January 2007, has a few ninja feats, some of which expend uses of the ninja's ki power to activate their effects. Issue 349, November 2006, has a Poisonmaking Guide on pages 86 and 87 that could be useful to ninja characters.