You have missed out the code for MainPage, but I'm going to assume the open() method performs a cy.visit() which changes the win returned from cy.window(), so you are stubbing too early.

See Window Before Load shows how to stub correctly using the window:before:load event.

You also do not need the noisy assignment to win, at least for static methods.

MainPage

import MyCustomClass from './my-class'

class MainPage {
  public open(): void {
    cy.visit('https://example.com')
      .then(() => {
        // make sure you console.log after the window:before:load event
        // i.e after the stub is set up
        console.log('From MainPage (myMethod): ', MyCustomClass.myMethod())
      })
  }
}
export default MainPage;

Test

let mainPage: MainPage;
describe('stubs the static method', () => {

  beforeEach(() => {

    Cypress.on('window:before:load', () => {
      console.log('From "window:before:load" event')
      cy.stub(MyCustomClass, 'myMethod').returns('stubbed static value')
    })

    mainPage = new MainPage()
    mainPage.open() 
  })

  it('Test something', () => {
    console.log('From the test: ', MyCustomClass.myMethod()) 
    expect(MyCustomClass.myMethod()).to.eq('stubbed static value')
  })
})

Cypress runner

Console