The course is irrelevant really, you'll do equally well at either. You need to choose based on where you want to live for three years.
King's is beautiful and old, which has the downside of having a lot of tourists running around. Also, quite a bit of King's accommodation is off-site, although there's probably enough on-site for that not to be too much of a problem. It has a really nice bar, and hosts quite a few nice events like the King's Jest and the King's Affair. It has the reputation for being the left-wing college, and has one of the highest proportions of state school students in Cambridge. Its formal hall happens once per week, costs £14 a pop (relatively expensive) and sells out really quick, since guests aren't permitted (so people sell off their tickets to people from other colleges). Also, with the left-wing reputation comes various non-traditions, e.g. you don't wear gowns for anything (except maybe graduation).
Downing is newer, but still a good 200 years old or so. Its architecture is quite different from King's, and if you go there you'll see a lot of pillars and fewer tourists. The formals at Downing are still fairly hefty (£10 or so I think) but they're nice. There's a lot of accommodation on-site or nearby which is something you might want to take into consideration. You'll also find slightly more tories and private school students at Downing than at King's (but nowhere near as many as at, say, St John's). I don't really know that much more about Downing to be honest. Oh, and the bar isn't that great... it's a separate building with horrible seats in it, kind of like a portacabin, and it's pricey.
Both colleges are right in the centre of town (but at different sides of the town centre). They do almost identically academically in the Tompkins table (Kings was 14th and Downing 15th this year) and they're both roughly equidistant from where most NatSci lectures will be. NatSci practicals are located a couple of miles out of the town centre and are probably marginally closer to King's, but not so much that it would make much of a difference.
Hope this helps.