Joe Hamrahi at   Baseball Daily Digest has grouped the different Top Rankings for each team to a spreadsheet here in Excel workbook form, with tabs at the bottom for each division, headings for each ranking body (Fangraphs, BP, Hardball Times, etc) and tabs for different Leagues, for instance:

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Eastern League

1. Pedro Alvarez, 3b, Altoona (Pirates)

2. Madison Bumgarner, lhp, Connecticut (Giants)

3. Kyle Drabek, rhp, Reading (Phillies)

4. Carlos Santana, c, Akron (Indians)

5. Jesus Montero, c, Trenton (Yankees)

6. Domonic Brown, of, Reading (Phillies)

7. Junichi Tazawa, rhp, Portland (Red Sox)

8. Wilson Ramos, c, New Britain (Twins)

9. Michael Taylor, of, Reading (Phillies)

10. Brad Lincoln, rhp, Altoona (Pirates)

11. Hector Rondon, rhp, Akron (Indians)

12. Josh Reddick, of, Portland (Red Sox)

13. Ike Davis, 1b, Binghamton (Mets)

14. Marc Rzepczynski, lhp, New Hampshire (Blue Jays)

15. Jose Tabata, of, Altoona (Pirates)

16. Scott Sizemore, 2b, Erie (Tigers)

17. Jake Arrieta, rhp, Bowie (Orioles)

18. Nick Weglarz, of, Akron (Indians)

19. Zach McAllister, rhp, Trenton (Yankees)

20. Brandon Snyder, 1b, Bowie (Orioles)

Kind of neat to click around & check out.

Not everything in the "League" section is completely updated (it still has Cutch @ Indy), but it does have players ranked in different leagues as they move around, so whereas Pedro is #1 in the Eastern League, it also has him as #3 in the Carolina League, and Tabata #13 in the Int'l League, etc.

Perhaps you all were already aware of these sites, though.