The Wigan owner made his comments as he paid tribute to former Blackburn team-mate Ronnie Clayton, who died last week.
A one-club man, Clayton made 665 appearances for Rovers and won 35 England caps.
Whelan would like to see more local lads playing for their local teams - but knows he needs to change the mentality of parents.
He said: "If any youngsters become available the dad wants to say, 'My son plays for Manchester United.'
"I keep trying to give advice that youngsters will do much better playing for Wigan, Bolton, Blackburn and Burnley because the openings there are much better.
"When you go to Manchester United you are taking on the whole world. It is the same at Liverpool and Manchester City.
"All the people in and around Lancashire who want their youngsters to play for Liverpool and Manchester United should think twice."
With manager Roberto Martinez at the helm, Whelan has promised he would not stand in a promising player's way if a top team came calling.
Whelan said: "Roberto now wants youngsters and we have been signing youngsters. We bring them on , get them going and push them up.
"I will not stop those players going to the top six teams in the world or the Premier League. So, mums and dads, put your sons in clubs where they will get an opportunity."
Whelan said Clayton would have graced any team on the planet and added: "What would he have been worth today? The kind of player he was Ron would have been priceless.
"Ron could not stop running, he was up and down the pitch the whole game. What any team would give to have him in their midfield. He could play in the finest team in the world."
Whelan suffered another devastating blow over the weekend with the death also of John Benson.
Benson carried out a variety of tasks at Wigan, including those of manager, assistant manager and general manager.
Whelan said: "John was a great fellow and got us success. He was a quiet man but very effective in his work.
"He told me three weeks ago he had been diagnosed with cancer and I was shocked. It is awful to lose a pal like that."