Class-Definition Comparison
Using prototype is useful for polymorphism. If you want to create another class, eg. ColourfulPoint, you can use this code:

ColourfulPoint.prototype = Object.create(Point.prototype);

to make your new class inherit all the methods of Point.
The first method (using only a constructor) is a way faster (at least in Firefox and Chrome) than the prototype one. Take a look at the test.
Unless you intend to create polymorphic classes, use the first one.