How well do you fit the entry criteria of each? Are secondaries in your area generally oversubscribed?
I think you need to take the possibility of travelling out of the equation for this - it's still years away, and if for any reason it doesn't happen and you want your DC in school, then your choice now might have to stretch to the entire secondary years.
If you think your DS is likely to thrive in an academic rather than a vocationally oriented school then it's between 1 and 2. It's also likely that the range of extra curricular activities will be better at a typically sized school than a small one.
Is there any chance you can dig a bit into why schools 1 and 2 have reputations of 'snooty' and 'rough'? Such reputations linger, but might not always be well rooted.