By the point you are sabotaging the substation you have passed the point of no return and can no longer switch your ending to NCR. You may still switch between the Yes Man (independent) or House endings, if he is still alive.
You can read more about the NCR’s point of no return from the forewarning Don’t tread on the Bear quest page.
More specifically, you became locked out of the NCR ending when you either replaced House with Yes Man, met all the factions for Yes Man, or dealt with the Omertas for Mr. House.
You must reload a save to choose an alternate path to remain in the NCR’s good graces and end the game in their favor. If you sneak in while disguised as an NCR soldier or while using a stealth boy you won’t suffer reputation loss after the sabotage, but you still will not be able to proceed with the NCR quest line.