Detecting movement

You could try just increasing the threshold value > 50 in the above code? Or how close is the magnet nearby? You could make the threshold value dependent on the strength of the magnetic field - since the noise in the reading may well be proportionate to the size of the field.

Otherwise if the readings keep varying randomly you could try keeping a short term average of the readings and comparing that to work around noise? This isn't tested, but something like it should work:

var avr = Puck.mag(); // long average
var savr = Puck.mag(); // short average
var magDiff;
Puck.on('mag', function(xyz) {
  // update short average
  var dx = xyz.x-savr.x;
  var dy = xyz.y-savr.y;
  var dz = xyz.z-savr.z;
  savr.x += dx/2;
  savr.y += dy/2;
  savr.z += dz/2;  
  // work out difference in field
  var dx = savr.x-avr.x;
  var dy = savr.y-avr.y;
  var dz = savr.z-avr.z;
  magDiff = Math.sqrt(dx*dx+dy*dy+dz*dz);
  // update average
  var dx = xyz.x-avr.x;
  var dy = xyz.y-avr.y;
  var dz = xyz.z-avr.z;
  avr.x += dx/8;
  avr.y += dy/8;
  avr.z += dz/8;  
  LED.write(magDiff > 50); // this value might need lowering
});
Puck.magOn();

You could also do a median filter, which is relatively easy to do with the built-in array.sort.