If the NFL were to finish today, there's no doubt in my mind that Manning, Brady, Brees and Rodgers would be considered better QBs than Wilson due to their body of work, but RIGHT NOW? There's no way in hell I could consider Brady or Manning better QBs than Wilson.
Manning is as much a product of his environment as Wilson is, his receiving corps turned short passes into long touchdowns consistently last year (which is why when faced with a defense that tackles well in the Superbowl he faded), he simply doesn't have the arm to take the top off anymore.
Brady too is now on the decline from the very top. People point to his receiving corps last year as the reason he had a down year, but whilst our own receiving corps is "sneaky good", it's easy to forget that Wilson's rookie season had him open the season with Braylon Edwards, Charly Martin and Ben Obomanu on the gameday roster, and finished the season with Deon Butler and a rookie Jermaine Kearse replacing the three of them - and he still threw more touchdowns and less interceptions than Brady did last year.
Whether he is better than Rodgers or Brees is up for debate, at the moment neither of them are showing significant signs of decline, but both have had far greater passing options than Seattle has (until now, at least). Still, to this day I've yet to see either of them do something and think "wow, I wish Wilson could do that", whereas I have seen both in situations and thought "Wilson wouldn't do that", or "Wilson would have avoided that sack". The defense has been able to cover up some of Wilson's poorer games, however, every QB has poor games - remember when Brees went to Atlanta in 2012 and threw FIVE interceptions?
I don't think Wilson had a single poor game last year - he had some where he didn't play well for times and the stats suggest he had a poor game, e.g. Tampa Bay and Houston. However, anyone that watched those games will remember Wilson simply taking the ball on the ground against Houston and destroying them, or coming back from 21 points down against Tampa Bay to win in overtime. He didn't have the best game against Arizona, but even then he looked poised to drive down the field for victory before the refs made a poor call on the incomplete interception.
You can look back at his rookie year and see the poor stats against SF and think he had a poor game, but again that's a game where if not for drops by the receivers he would have had a nice game - and against the toughest opposition in the league. You really have to go back to that game against the Rams where he had 3 unfortunate interceptions, but really didn't play well all around anyway, but that was the 4th start of his career, he is literally 850% more experienced as a pro since that game in terms of competitive games.