Only the ball was placed to the outside shoulder because the safety was closing in. It wasn't a perfect throw, but if you can find me a quarterback that has been perfect on 100% of his crunch time throws in his career, I'll buy a ticket, fly to Seattle, and let you punch me in the face.
As it stands, the ball hit Welker in the hands. It should have been caught and the game should have been over at that point. The Giants, as is usually the case when they play the Pats, got lucky. They also got lucky by having numerous lost fumbles bounce away or, literally, between surrounding Patriots throughout the game. That's why they were able to sustain the onslaught in the second half in just enough time for Eli to throw up a prayer through double coverage.