There is zero question they are set in the same universe.
In Assassins Creed, Olivier Garneu is the director of Abstergo Entertainment. You see and interact with him multiple times. Part of the way through the game he leaves to go to an investors meeting in Chicago.
In Watch Dogs when you complete the final optional Criminal Convoy your target is Olivier, and he's being transported by Abstergo gards. Assassins Creed IV and Watch Dogs are happening simultaneously. I doubt the games will ever cross paths but there is zero debate whether they are in the same universe considering literally a major character in AC4 appears in Watch Dogs exactly where he should be when he leaves AC4.