The best college in Oxford for any subject is the college from which you obtain an offer. Apply to the college that you would like to join. If you obtain an offer (and that is always a big if), there is approximately a one in four chance that the offer will come from a college other than the one you applied to.
When you apply for a job or for a postgraduate course, no one will say "Sorry, mate; if you had studied Chemistry at X College, Oxford, instead of at Y College, Oxford, we'd have given you the gig, but because you were at Y College, we are rejecting you."