I’m going to echo many posters and ask: have you already gotten into both? Otherwise, there’s not really much of a point asking the question…
But to answer, here are some differences between the two:
Swat is a lot smaller compared to UChicago (although both are very small relative to other places). If I recall correctly, Swat’s undergrad population is around 1500, whereas Chicago’s is around 5000.
While both schools are very rigorous academically, I think Swat is even more so. It is quite notorious for its extremely heavy workload, which could be a boon or a curse depending on who you are. If you really want to learn, and just learn, Swat is probably the environment that fits you better. If you want the more traditional “college experience”, with some free time, some time to join clubs/organizations/etc, Chicago is for you.
Swarthmore is part of the Tri-College Consortium, which allows you to cross register at Haverford and Bryn Mawr. If you want to explore that option, you might consider Swat over Chicago.
UChicago is an urban campus at the heart of the city, whereas Swat is really the deep 'burbs. So, again, depends what kind of person you are. I assume Chicago would get you more opportunities, city life, etc, but if you want the traditional, beautiful campus Swat is more like that.
All in all, they’re very different places. If you haven’t done so already, I would try to arrange a campus visit. If you can’t visit both, try visiting one, or even (again, if you haven’t done so) visit one suburban and one urban campus just to get the feel of the two. I’ve seen a lot of people who loved places like Swat on paper, visited, and realized they could never live there for four years (and vice-versa with Chicago)!
Also, for the majors you suggested, the two schools are pretty much equal. I would venture to say that Chicago’s chem department is slightly better than Swat’s? But I’m no expert.
Anyways, if you can afford to ask this question, you’ve either gotten in or you’re pretty damn confident about your chances of getting into both. So, let me just say that if you like both schools, you can’t go wrong at all. They’re both great and as long as you think they fit you, as long as you think they can both be places you can grow academically and personally, you’ll succeed.