Which is a better Kyogre?

If maxing out, the 96% should be better. Otherwise, the 93% will save you some resources to reach breakpoints

96% for me. You won't notice the missing 1 IV for attack when fully powered up.

The 93% is better. Kyogre can't defend, so it is all about maximum DPS which you will get with the 15 att.

1 att IV >> 2 def IV any day in the current meta for legendaries.

Of course, in most real life scenarios they will perform almost 100% identically.

Both are excellent, it really doesn't matter much.

If you really want to split hairs, look at the break points and bulk points for specific matchups you want to do with it. If one or the other hits or misses a break point at level 40 or bulk point because of the missing stat, power up the other one. Most likely they will perform the same, and it doesn't matter.