It depends. Both seeds can be equally healthy and viable . So you make a choice which one you want to keep. You can wait actually keep both of them much longer in 3' pot and see which one is doing better. When I have 2 per 3" pot and I want to keep both I would separate them when they are up to 4 inches tall. By then the seedlings are not root bound yet in 3" pot.

BUT since you just want to keep one you can eliminate one of them much sooner.

Seysonn