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You should have different ninja slider IDs for each slider. Say you have given them the id ninja-slider and ninja-slider2. Then open the ninja-slider.js with Notepad, and edit it as below:
var nsOptions = {sliderId: "ninja-slider", ...};
var nsOptions2 = {sliderId: "ninja-slider2",...};
var nslider = new NinjaSlider(nsOptions);
var nslider2 = new NinjaSlider(nsOptions2);
// (the following should be remain untouched)
/* Ninja Slider ....
In this approach you have two Ninja Sliders in the same page.
Notice you also need to style them differently with the css selector #ninja-slider and #ninja-slider2.