Both good glass (I have them, too). I'd stick with the APO if it seems clear and solid. These are known to be best performing at relatively open apertures and I use mine at 5.6 mostly as with my equipment and materials, it gives me about the right exposure times, allowing for some dodging/burning. You will have very little depth of field forgiveness at open apertures, so aligning your enlarger becomes doubly important for extracting what that good APO lens can deliver.
I have multiple enlargers. They use different mounts. The APO is already mounted on another enlarger. For this one I just received a new mount and is going to replace the Nikkor 50mm with either the Schneider or Rodenstock. Both are good and I have no opinion...
A photo amateur
Sinar P2/F2/Nikon F100/Bronica ETRSi/GS/Saunders 4550XLG/Jobo CPP2/CPE+/Colorline 7000
If any of your enlargers are Omega D series, some of the 50mm lenses work better than others with some of the mounting systems.
“Photography is a complex and fluid medium, and its many factors are not applied in simple sequence. Rather, the process may be likened to the art of the juggler in keeping many balls in the air at one time!”
Ansel Adams, from the introduction to The Negative - The New Ansel Adams Photography Series / Book 2