Probably not Eton (one of my DC is there). It's absolutely bloody marvellous all round, but I wouldn't say that football is prized above all else. My DS hasn't played football since he went there (for which his is mightily grateful, as he hates it).
I think you might find, OP, that any school that really pushes football might be a bit less of an academic power-house. I don't mean that in a bad way - that's just how it is. I know several boys who have boarded at Sedbergh (all went there for its sport), and have loved it - though, again, it's ok academically, but not 'top notch'. I also know people who've had boarders at Millfield (again, all sporty - and, again, not especially bright), and they've all loved it.
As Happygardening says, I wouldn't choose Winchester for its football provision (it's a brilliant school, though - again, I know several people who have had children there).
FWIW, I don't think I'd send any child to a school where only a few children board, though that's not what you're asking.