What we can go on:

-In their first fight, the FF8 intro, they were about even.
-in their second fight at the end of Disc 1, Squall alone manages to defeat Seifer.
-Squall and two other party members take on and beat Seifer 2 more times. (game mechanics aside, You do confront Seifer with 3 people so storywise, I say it was 3 on 1)
-Seifer owned Odin in one shot.

So, who was stronger?