I'll freely admit that Thomas, when playing at his very best, was better than Stockton at his very best, but, Thomas is not capable of playing at his very best always, which Stockton was.
In a seven game series, I would expect Thomas to have a better game than Stockton at least once, perhaps twice, but over the 7-game series, Stockton's numbers would certainly be better than Thomas's numbers.
The thing with Stockton is that he was consistent. He always played at a high level, where as Thomas was very streakly, even within games. He could be cold all game, then go on a tear in the third or forth quarter, and in those instances, that level of play was as high as any level of play ever seen in teh NBA, but he couldn't keep that up. With Thomas, you always knew that he would give a 100%, like Stockton, but with THomas you never knew is that was gong to be 18 points on 6-19 shooting with 8 assists and 5 turnovers, or 31 points on 14-20 shooting with 9 assists and 2 turnovers. With Stockton, you always know what level of play you are going to get from him.
And that said, I would take Stockton in his prime over Thomas in his prime any day of the week. Liek I said in an earlier post, the only thing Thomas did more of was socring, and that's because he shot so much more. Stockton got more career points with fewer FGA. I think that had Stockton been playing his prime in Detroit when Thomas was, Detroit would have won three in a row, and they wouldn't have been swept by the Bulls in 91.