In terms of productivity, Southampton.
In terms of ability, probably Liverpool, Man Utd or Chelsea.
In terms of facilities, Man City.
My favourite player in my teams (Man Utd) academy would be Andreas Periera. Looks really exciting and reads the game brilliantly, should have a big career ahead of him.
English youth academies contain masses of talent, tons of it. The problem is getting them into the first team when the attitude of English football, across the board is so averse to training and player growth.