Here are two rankings by the [FCBarelona.com][1] official page and Spanish paper [Sport][2], 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][3] in Santos: 643 goals

As per 11 September 2017,

 1. [Gerd Müller][4] for Bayern München: 525(564<sup>1</sup>) goals

 2. [Jimmy McGrory][14] for Celtic: 522 goals

 3. [**Lionel Messi**][5] for Barcelona: 513 goals

 4. [Uwe Seeler][15] for Hamburger: 507 goals
    
 5. [Eusebio][6] for Benfica: 473 goals

 6. [**Cristiano Ronaldo**][8] for Real Madrid: 407 goals

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 7. [José Águas][7] for Benfica: 379

 8. [Nené][9] for Benfica: 359 goals

 9. [Ian Rush][10] for Liverpool: 349 goals

 10. [Telmo Zarra][11] for Athletic Bilbao: 336 goals
 
 11. [Raúl][12] for Real Madrid : 323 goals
                
 12. [Alfredo Di Stéfano][13] for Real Madrid: 307 goals

<sup>1</sup> 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.

  [1]: https://www.fcbarcelona.com/football/first-team/news/2016-2017/leo-messi-draws-level-with-eusebio-for-number-of-goals-with-the-same-club
  [2]: https://scontent.fsof3-1.fna.fbcdn.net/v/t1.0-9/15094361_728606243964390_8453748507702950649_n.jpg?oh=d3b68ec97ae2519a13d8d802e76f4e6f&oe=58B32071
  [3]: https://en.wikipedia.org/wiki/Pel%C3%A9#Club_2
  [4]: https://en.wikipedia.org/wiki/Gerd_Müller#Club_career_statistics
  [5]: https://en.wikipedia.org/wiki/Lionel_Messi#Club
  [6]: https://en.wikipedia.org/wiki/Eus%C3%A9bio#Career_statistics
  [7]: https://en.wikipedia.org/wiki/Jos%C3%A9_%C3%81guas#Statistics
  [8]: https://en.wikipedia.org/wiki/Cristiano_Ronaldo#Career_statistics
  [9]: https://en.wikipedia.org/wiki/Nen%C3%A9_(footballer,_born_1949)
  [10]: https://en.wikipedia.org/wiki/Ian_Rush#Career_statistics
  [11]: https://en.wikipedia.org/wiki/Telmo_Zarra
  [12]: https://en.wikipedia.org/wiki/Ra%C3%BAl_(footballer)#Career_statistics
  [13]: https://en.wikipedia.org/wiki/Alfredo_Di_St%C3%A9fano#Club
  [14]: https://en.wikipedia.org/wiki/Jimmy_McGrory
  [15]: https://en.wikipedia.org/wiki/Uwe_Seeler