Use min/max and padding.V2

If you use min/max padding is ignored thus to have padding increase min/max.

HTML

<script src="https://cdnjs.cloudflare.com/ajax/libs/jqPlot/1.0.8/jquery.jqplot.min.js"></script>
<div id="chart1" class="chart">

</div>

CSS

.chart {
  height: 200px;
  width: 400px;
}

//jquery.jqplot.css

/*rules for the plot target div.  These will be cascaded down to all plot elements according to css rules*/

.jqplot-target {
  position: relative;
  color: #666666;
  font-family: "Trebuchet MS", Arial, Helvetica, sans-serif;
  font-size: 1em;
      height: 300px;
    width: 400px;
}


/*rules applied to all axes*/

.jqplot-axis {
  font-size: 0.75em;
}

.jqplot-xaxis {
  margin-top: 10px;
}

.jqplot-x2axis {
  margin-bottom: 10px;
}

.jqplot-yaxis {
  margin-right: 10px;
}

.jqplot-y2axis,
.jqplot-y3axis,
.jqplot-y4axis,
.jqplot-y5axis,
.jqplot-y6axis,
.jqplot-y7axis,
.jqplot-y8axis,
.jqplot-y9axis,
.jqplot-yMidAxis {
  margin-left: 10px;
  margin-right: 10px;
}


/*rules applied to all axis tick divs*/

.jqplot-axis-tick,
.jqplot-xaxis-tick,
.jqplot-yaxis-tick,
.jqplot-x2axis-tick,
.jqplot-y2axis-tick,
.jqplot-y3axis-tick,
.jqplot-y4axis-tick,
.jqplot-y5axis-tick,
.jqplot-y6axis-tick,
.jqplot-y7axis-tick,
.jqplot-y8axis-tick,
.jqplot-y9axis-tick,
.jqplot-yMidAxis-tick {
  position: absolute;
  white-space: pre;
}

.jqplot-xaxis-tick {
  top: 0px;
  /* initial position untill tick is drawn in proper place */
  left: 15px;
  /*    padding-top: 10px;*/
  vertical-align: top;
}

.jqplot-x2axis-tick {
  bottom: 0px;
  /* initial position untill tick is drawn in proper place */
  left: 15px;
  /*    padding-bottom: 10px;*/
  vertical-align: bottom;
}

.jqplot-yaxis-tick {
  right: 0px;
  /* initial position untill tick is drawn in proper place */
  top: 15px;
  /*    padding-right: 10px;*/
  text-align: right;
}

.jqplot-yaxis-tick.jqplot-breakTick {
  right: -20px;
  margin-right: 0px;
  padding: 1px 5px 1px 5px;
  /*    background-color: white;*/
  z-index: 2;
  font-size: 1.5em;
}

.jqplot-y2axis-tick,
.jqplot-y3axis-tick,
.jqplot-y4axis-tick,
.jqplot-y5axis-tick,
.jqplot-y6axis-tick,
.jqplot-y7axis-tick,
.jqplot-y8axis-tick,
.jqplot-y9axis-tick {
  left: 0px;
  /* initial position untill tick is...

JavaScript

$(document).ready(function() {
  var valuesToRemove = ['-10', '210']; //must be given as string
  $.jqplot.postDrawHooks.push(function() {
    var children = $("div.jqplot-axis.jqplot-yaxis").children('div');
    console.log("children.size() = " + children.size());
    $(children).each(function(index) {
      var child = $(this);
      //if having problems with indexOf method in IE see this SO answer http://stackoverflow.com/a/1181586/613495
      if (valuesToRemove.indexOf(child.html()) !== -1)
        child.hide();
    });
  });

  var datos = [
    [3, 4],
    [2, 2]
  ];
  $.jqplot('chart1', [datos], {
    axes: {
      xaxis: {
        min: 1,
        //was '1'
        max: 5,
        //was '5' 
        tickOptions: {
          show: true,
          showLabel: true
        }
      },
      yaxis: {
        max: 1,
        min: 200,
        ticks: ['210', '200', '150', '100', '50', '1', '-10'],
        tickOptions: {
          formatString: '%i'
        }
      }
    }
  });


});