ES2016 Class, Sinon Stub Constructor

You need to spy instead of stub,

sinon.spy(Foo.prototype, 'constructor');

describe('Example', () => {
  it('should stub super.constructor call', () => {
    const costructorSpy = sinon.spy(Foo.prototype, 'constructor');
    new Bar();
    expect(costructorSpy.callCount).to.equal(1);
  });
});

*****Update****** Above was not working as expected, I added this way and is working now.

 describe('Example', () => {
    it('should stub super.constructor call', () => {
      const FooStub = spy(() => sinon.createStubInstance(Foo));
      expect(FooStub).to.have.been.calledWithNew;
    });
 });

You'll need to setPrototypeOf the subClass due to the way JavaScript implements inheritance.

const sinon = require("sinon");

class Foo {
  constructor(message) {
    console.log(message);
  }
}

class Bar extends Foo {
  constructor() {
    super('test');
  }
}

describe('Example', () => {
  it('should stub super.constructor call', () => {
    const stub = sinon.stub().callsFake();
    Object.setPrototypeOf(Bar, stub);

    new Bar();

    sinon.assert.calledOnce(stub);
  });
});