Here is a function that calculates the current position of an element within the viewport:
/**
 * Calculates the position of a given element within the viewport
 *
 * @param {string} obj jQuery object of the dom element to be monitored
 * @return {array} An array containing both X and Y positions as a number
 * ranging from 0 (under/right of viewport) to 1 (above/left of viewport)
 */
function visibility(obj) {
    var winw = jQuery(window).width(), winh = jQuery(window).height(),
        elw = obj.width(), elh = obj.height(),
        o = obj[0].getBoundingClientRect(),
        x1 = o.left - winw, x2 = o.left + elw,
        y1 = o.top - winh, y2 = o.top + elh;
    return [
        Math.max(0, Math.min((0 - x1) / (x2 - x1), 1)),
        Math.max(0, Math.min((0 - y1) / (y2 - y1), 1))
    ];
}
The return values are calculated like this:

Usage:
visibility($('#example'));  // returns [0.3742887830933581, 0.6103752759381899]
Demo: 
function visibility(obj) {var winw = jQuery(window).width(),winh = jQuery(window).height(),elw = obj.width(),
    elh = obj.height(), o = obj[0].getBoundingClientRect(),x1 = o.left - winw, x2 = o.left + elw, y1 = o.top - winh, y2 = o.top + elh; return [Math.max(0, Math.min((0 - x1) / (x2 - x1), 1)),Math.max(0, Math.min((0 - y1) / (y2 - y1), 1))];
}
setInterval(function() {
  res = visibility($('#block'));
  $('#x').text(Math.round(res[0] * 100) + '%');
  $('#y').text(Math.round(res[1] * 100) + '%');
}, 100);
#block { width: 100px; height: 100px; border: 1px solid red; background: yellow; top: 50%; left: 50%; position: relative;
} #container { background: #EFF0F1; height: 950px; width: 1800px; margin-top: -40%; margin-left: -40%; overflow: scroll; position: relative;
} #res { position: fixed; top: 0; z-index: 2; font-family: Verdana; background: #c0c0c0; line-height: .1em; padding: 0 .5em; font-size: 12px;
}
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<div id="res">
  <p>X: <span id="x"></span></p>
  <p>Y: <span id="y"></span></p>
</div>
<div id="container"><div id="block"></div></div>