The table below shows how many BFW (batting wins plus fielding wins from Pete Palmer, using the linear weights method) and how many Win Shares (WS), the Bill James stat, various players had in the NL during this period. The two lists are not necessarily the top 25 in either stat. I simply found all the players who had at least 1 season in the top 5 in BFW in these years and at least 1 season in the top 12 in WS, found their total for the 5 years and then ranked them. The BFW totals come from Retrosheet and the WS totals come from the electronic version of the book.
Santo completely dominates in BFW. The age number is given for players who are in the Hall of Fame and it is their age in 1964, with a June 30 cutoff. It may be cherry picking to make these comparisons since I am taking Santo's best 5 year period. But that is why I put the age of the other Hall of Famers in. Many of them were at an age where they could still be performing well. Also, below, I show the best 5 year periods for these other Hall of Famers (except Aaron and Mays) and Santo still does extremely well. I did not include Frank Robinson because he was traded to the AL prior to the 1966 season.
Santo is only 3rd in WS. But he only trails the leader, Mays, by 6. Santo had the following ranks in BFW in these years: 1, 2, 1, 1, 4. For WS, they were 3, 4, 4, 1, 10. Those ranks for both stats are only among position players. I guess not too many people noticed how well he did since his ranks in the MVP voting, among position players, were 8, 13, 9, 4, 17. Maybe he was hurt by the Cubs not winning any pennants.
I also tried to find the leaders in Wins Above Replacement (WAR) during those years from Sean Smith's site. Below are what are probably the top 5. I checked a few other players, but none of them came close to these five.
So only Willie Mays was better. Now the next table shows the best 5 year stretches for what I think are all of the Hall of Famers who played in the NL during these years, not counting Aaron and Mays. This is not limited to the 1964-68 years. It is the highest 5 consecutive years for each one of these players.
Santo is only topped in BFW by Joe Morgan. He is only tied for 3rd in WS. But that still means that he beats 6 Hall of Famers he played with and/or against. Three of them, Willie Stargell, Willie McCovey, and Lou Brock were elected in their first year of eligibility. Clemente would have had he not died and been elected right away under special circumstances.