Where to start? First, I’m a Reed graduate. Reed is lefty, but it’s also a college with a strong academic, intellectual ethos. You can be anything politically there. And you can definitely be gay. It’s one of the most gay friendly colleges that I know of. It would likely be an admissions “match” for the OP’s son. Small classes, based in many cases on what Reed calls the “conference” system and every place else calls “seminars.” The workload is extremely demanding, but the OP’s son can handle it, and would likely find the level of debate and discussion (the “intellectual” atmosphere) to his liking. My son applied and was accepted to Reed also.
An indirect measure of Reed’s intellectuality is that a very large percentage of graduates go on to earn PhD’s. You might look at this source to find other colleges with this characteristic:. It helps to identify colleges that have a strong academic, intellectual program: https://www.reed.edu/ir/phd.html and https://www.reed.edu/ir/phdrank.html.
Second, my son attended UChicago. His stats were similar to your son’s. His first rule was that he wanted a college where it is “safe to be a thinker.” Chicago fits that to a T. He majored in economics, which involves heavy-duty applied math and statistics. He all-but-minored in political science. One doesn’t have to major in math to get a strong applied math exposure. If your son attended Chicago he’d have a chance to enjoy courses in many majors with outstanding faculty (in social sciences, biological sciences, and other fields). Chicago is not especially “competitive” in the sense that the OP’s son might think of it. There’s a strong culture of open inquiry and hard work, not dog-eat-dog competition and grade grubbing. My son abhors intellectual “poseurs,” and that’s one reason he chose UChicago. It doesn’t hurt to be gay at Chicago. After all, Nate Silver attended and he is gay.
Yes, Chicago is a big city, but that was one reason why my son chose to attend Chicago. He made it a point to get well off campus at least once a week, weather to attend major league sporting events (baseball in particular) or to enjoy some of the other venues in the city. Public transportation is very good, and so it’s not difficult (or expensive) to get around.
Third, I agree with your son’s thinking about Williams. My son was admitted there but really didn’t like Williams or Williamstown when he visited. Too tiny. Too isolated. Too jocky. Academics would have been strong but the isolation and smallness of the place would have bothered him. In contrast, when he visited a friend at Amherst, which has similar academic strength, he found the atmosphere to be more diverse, in part because Amherst the town was much larger and it also had a large contingent of students from UMass-Amherst. My son didn’t apply to Amherst, but would likely have enjoyed attending.
I have a brother-in-law who attended Colby; also a former student of mine attended as well. It’s a good school but academically a grade below Reed, Chicago, Amherst, and Williams. But in Maine I think your son might like Bowdoin and could give that a look.
In the Philadelphia area, Haverford has a very good academic reputation and is not a dog-eat-dog atmosphere. On the other hand, Swarthmore has a stronger academic reputation but is also harder to get into and is highly competitive (I am told).
I think Oberlin, Grinnell, and Carleton are also very much worth looking at. Of those colleges, my son was admitted to Carleton, but never visited it. He didn’t apply to Oberlin or Grinnell.
I can perhaps provide more information if you have any questions of me.