The ones that occur to me first are Clark, Wesleyan U (a little smaller than mid-sized, but fits a lot of the other criteria – check out their College of the Social Studies), American U, and George Washington. Skidmore is not urban, but Saratoga Springs is a lively and active small town with lots to do. If he’s willing to travel farther, check out Macalester.
Btw – national achievement in an EC is awesome – it doesn’t matter if it’s not related to a major. High school should be a time to explore interests, not to find activities just to position yourself for a major or profession, so it’s fantastic that he’s found something that he’s really been able to dig into regardless of where (if anywhere) it takes him.
ETA: If he’s willing to consider a small school like Oberlin, then what about Vassar? Similarly progressive and trans-friendly, but in a more welcoming state.