My personal preference of these two performances is the earlier one, performance-wise. To me, Bernstein has greater control in his earlier performance than in the later DG one, though he does wear "heart-on-sleeve" in both performances. There are things about the SACD remastering of the Sony/Columbia that are good and things that are bad. The good: You can hear a greater sense of the performing venue, as well as air around the instruments. Increase in dynamics is only minimal. The bad: The organ at the conclusion of the work is not as well heard on the SACD remastering as in the initial one by Columbia Masterworks, plus the extra cost to only gain minimal returns from purchasing the SACD remastering is not worth it.
Bottom line: You're better off buying the entire regular CD set of the entire Bernstein Sony/Columbia cycle on the Carnegie Hall label for $21.00 less than you would pay for the Japanese SACD version of M2 alone (as of this writing). Both the Japanese SACD of M2 and the entire cycle on Carnegie Hall are from the same DSD remasterings by Andreas K. Meyer.
I'm unable to comment on his later M3 performance on DG, because I don't have it. I do like his earlier Sony/Columbia performance.
Wade