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Here are two rankings by the official page and Spanish paper Sport, which are used as the most reliable ones (for the retired players).
Pele's goals are not scored in Europe, anyway they are pointed as an ultimate achievement.

  • Pelé in Santos: 643 goals

As per 8 October 2018,

  1. Lionel Messi for Barcelona: 563 goals

  2. Josef Bican for Slavia Prague: 534 goals

  3. Gerd Müller for Bayern München: 525(5641) goals

  4. Jimmy McGrory for Celtic: 522 goals

  5. Uwe Seeler for Hamburger: 507 goals

  1. Eusebio for Benfica: 473 goals

  2. Cristiano Ronaldo for Real Madrid: 450 goals

  1. José Águas for Benfica: 379

  2. Nené for Benfica: 359 goals

  3. Ian Rush for Liverpool: 349 goals

  4. Telmo Zarra for Athletic Bilbao: 336 goals

  5. Raúl for Real Madrid : 323 goals

  6. Alfredo Di Stéfano for Real Madrid: 307 goals

1 Gerd Müller has scored 39 more goals in 1964-65 season for Bayern in Regionalliga Süd, which existed as the second tier of the German football league system from 1963 to 1974.