Some possible explanations:

1. He went out with his buddy Al in a bar and Al got drunk and confessed it.

2. He had the Sicilian cunning even at 10 years of age (or so) and he immediately understood what was about to happen when Connie told him to get off the boat.

3. Kay told him in order to make him leave his father.

4. He knew it all along - was following orders by Michael to keep Fredo close. This is the way he "made his bones".

5. Everybody knew (this is the most plausible answer by far). But then what's the point that Tony, in particular, knew about it?