Ranking these guys as far as clay court prowess is very tough. They are all one-time French Open Champions. Keep in mind that if we give Federer "extra credit" for losing to an all-time great such as Nadal, a guy like Vilas should get some benefit for having to face Borg during Borg's reign. Vilas dropped 2 finals at the FO to Borg and 1 more to Wilander in 1982 (3 FO finals, 1 FO title).
Now, Agassi, also has 2 FO finals he lost, but he lost to Gomez and Courier (also really good clay courters, but not at Nadal's level).
Since all these guys have 1 FO title, I've listed total number of total clay court titles as a preliminary "tiebreaker". Looking at the list of players, ranked by total number of clay court titles, I'd put Federer at about 5 on the list, after giving him some extra credit since he plays in Nadal's era, but he is still pretty far behind a few of the other guys in terms of total clay court titles.
These guys at the top should get credit for winning many clay court titles, besides just the 1 FO title. So, I wouldn't rank them behind Federer just because they played in "earlier years". Will a 1 time FO champion in say 10 years NECESSARILY be better than Federer because of "natural evolution" of the Sport? I wouldn't think so. On a given day, Federer is quite dangerous on clay, but his results are not better than many great clay courters. It depends on what you want to emphasize. Just like any comparison between players of different era, this is subjective and objective. If a Federer fan wants to place Federer at the top of the list, he/she needs to give some reason as to why. Just because he is a "current" player is not enough in my opinion. Will players 10 years from now "automatically" be better than the guys at the top today? Not necessarily, in my opinion, but there will likely be changes to how the Game is being played at the highest level, driven by changing techniques, playing style, technology, and the sheer competition among the top guys.
Here's my list with just these players involved. Let's remember that guys like Courier and Bruguera have 2 FO titles and are not on this list at all.
1. Guillermo Vilas - 46
2. Thomas Muster - 40
3. Ilie Nastase - 28
4. Carlos Moya - 16
5. Roger Federer - 9
6. Andres Gomez - 16
7. Albert Costa - 13
8. Yannick Noah - 12
9. Juan Carlos Ferrero - 11
10. Adriano Panatta - 8
11. Gaston Gaudio - 8
12. Andre Agassi - 7
13. Michael Chang - 5
14. Yevgeny Kafelnikov - 4
15. Andres Gimeno - 3