Which Rayquaza would you choose?

If you're talking about maxing out your Rayquaza, the missing 2pts of attack really won't make any difference at all, given that Ray's attack stat is already so high. Having 15 IVs for its HP/DEF are typically more important, as Ray really lacks in the bulk department.

Go with the 96%. The other two are really sub par IVs.

I assume you're looking for something to take on Palkia with? I'm normally in the same boat with 15a Pokemon, but consider the 96% Ray only misses the following select breakpoints:

- Ultra friends no weather (15a required)
- Good friends w/windy weather (14a required)
- Ultra friends w/windy weather (15a required)

I'm going to assume at this point you regularly raid with people who you share best friend status? If that's the case, a 13a Rayquaza can meet the last Dragon Tail breakpoint at L37 with or without weather. Missing those few breakpoints likely won't happen if your endgame is to max it. Go with the 96% unless you think those few cases will apply to you.