Rooney has scored 16 goals for United this season yet against Stoke he was moved back into a defensive-midfield role alongside Michael Carrick.
Shearer told The Sun: "I have always said that Rooney would be the best player on the pitch wherever he plays, bar in goal.
"Right now, that is being tested, too. He has gone from the main frontman, to the supporting role in behind Van Persie, to out wide and a deep-lying midfield role.
"People will say that he is not in their class.
"But three or four years ago he was being talked about in the same breath.
"He is 27 and these should be the best years of his career coming up but he is not at the level we all expected he would be.
"He has to sit down with his advisors in the summer and ask himself whether or not a move would be beneficial.
"He is already at a great club with a great manager but things just don't look rosy to me."