Of course Krillin. Saiyan saga Vegeta's level was 18,000 whereas Krillin could fight nearly on par with a Cell Jr. Which was around the level of a ssj1 at the time (with a frieza saga ssj1 level being 150,000,000.) at that was during only the cell saga. Even back in the the aftermath of the frieza saga, Krillin was already stronger than most Ginyu force members whereas Vegeta was weaker than all but Guildo with his level at that point being 30,000.
Sorry, but Krillin was getting raped by the Cell jr that he was unlucky enough to go up against.
As for the fight, Krillin stomps. He wasn't far off end of saiyan saga Vegeta after he had his potential unlocked by Guru, and he continued to train until the end of the Cell saga, and then continued when he was in otherworld (he was even shown to be on the same level as some of them).
I think end of Freiza saga Vegeta would have been a better matchup.