The more I think about it, the more difficult I think the list is indeed and the more I change my mind.
I think at this point in time it is indeed about 1) Di Stefano and 2) Cristiano Ronaldo and then about players who wouldn't look out of place in TOP5 or TOP10.
Raul, Ramos, Puskas, Benzema, Modric, Gento would not look out of place in, let's say, TOP10. It is fair to say that there is some recency bias with Benzema, but it's also fair to say that Benzema's career at Madrid was already extraordinary before, and that he probably deserved to be in Top 10 had he retired a couple of years ago. Maybe we need to wait until Benzema and Modric end their careers so we can have a better perspective on things. The aspect that tends to be more underrated in the case of Karim is the things he has done as a 10, rather than as a 9. It was common for me to hear pundits (former coaches and footballers) on TV praise Benzema's performances in games ending 0-0 at half time in Liga games. Maybe stats, which are important themselves, are overshadowing everything unfairly these days.
I agree with some posters that Raul's legacy should be put into context and that it was probably damaged by his last years at the club, from 2004 onwards.
Other players like Pirri, Roberto Carlos, Michel, Butragueno, Casillas, Hugo Sanchez, Camacho, Stielike, Juanito, Redondo probably deserve to be in TOP20.