Top Shaq seasons:
2000
2001
2002
1998
1999
2003
1995
1994
Magic's best seasons:
1987
1990
1988
1989
1991
1986
1985
My list:
1. 2000 Shaquille O'Neal - clearly the best season in this comparison, unreal postseason performance.
2. 1987 Magic Johnson - a close comparison between 1987 and 2001. I think that Shaq peaked higher, but he had much lower lows than Magic ever had in 1987.
3. 2001 Shaquille O'Neal - Magic's defense in 1990 hurts his case a bit vs 2001 Shaq, but it's close.
4. 1990 Magic Johnson - my GOAT offensive season candidate. Simply the most complete version of Magic we've ever seen.
5. 1988 Magic Johnson - very close to the top 2 Magic seasons, some people blame him for slightly weaker RS scoring production but I don't find this problematic at all. He was still an outstanding scorer and it wasn't his most valuable trait.
6. 2002 Shaquille O'Neal - I could see a case for 1989 over 2002, but Magic's injury is too problematic to me here. Shaq had excellent postseason run after all, even if not as perfect as the top 2.
7. 1989 Magic Johnson - another ATG offensive performance from Magic, injury hurt his case a bit.
8. 1991 Magic Johnson - I know that Magic was a bad defender at this point, but his offense was as good as ever and Shaq's durability issues are too big for me to overcome.
9. 1998 Shaquille O'Neal - monster performace on per-possession basis, but missing so many games is a big no for me.
10. 1999 Shaquille O'Neal - Shaq defense was bad in this season, but it wasn't bad enough to exclude him from top 10.
11. 1986 Magic Johnson - the beginning of true Magic prime, improved jumpshot and post game are visible for anyone who is so much into watching old games as me

12. 2003 Shaquille O'Neal - another season with missed games and questionable defensive effort and missed games, but he was still a prime Lakers Shaq after all and I'd take that version of Shaq over pre-1986 Magic.
HM: 1985 Magic and 1995 Shaq
Another very close battle. It's not surprising to me - I have them next to each other on my all-time list. It's also clear that I value Magic's prime higher than Bird's and I know it's not a popular opinion.