The smaller one is quite possibly a female, but I wouldn't say it's a sure thing. I would say it will probably be the smallest when they're grown up. There usually isn't a huge difference in growth rates between males and females, just that females just slow down and reach their full adult size while males keep growing for a little while longer.
Hypothetically, let's say two of the bigger ones are males and the third big one and the small one are females. If I were you, I would pick the larger female. In all reality you want the two you keep to be at about an equal size and strength. If one is a lot smaller it is more likely to be bullied by the big one, and because of the stress that entails, chances of breeding would go down, while chance of disease and potentially death would go up. While it is highly unlikely that the larger would personally kill the smaller, the chances of a secondary effect of stress doing the damage should not be ignored.