Here are two rankings by the FCBarelona.com 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 15 March 2018,
Lionel Messi for Barcelona: 588 goals
Josef Bican for Slavia Prague: 534 goals
Gerd Müller for Bayern München: 525(5641) goals
Jimmy McGrory for Celtic: 522 goals
Uwe Seeler for Hamburger: 507 goals
José Águas for Benfica: 379
Nené for Benfica: 359 goals
Ian Rush for Liverpool: 349 goals
Telmo Zarra for Athletic Bilbao: 336 goals
Raúl for Real Madrid : 323 goals
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.