From Athens, I went on a day tour to Delphi by bus. The tour was excellent. I think I found it through Viator. I also went on a day trip by bus to Sounion (on the coast). It was very interesting, and offered great views of the Mediterranean. I took a day trip by plane to Santorini. I really liked Santorini. I don’t think it needs to be avoided as too touristy. True, parts of it are totally geared toward tourists, but many parts are very pleasant, and tend to not to be too crowded. Ancient Thera is an archaelogical site on near the highest point on the island, and there were very few people there when I visited–stunning views of the Mediterranean, in addition to the ruins. There is a black sand beach, a pink sand beach, and a white sand beach, all accessible by bus on the island. To the north (I think) there is a curving bay, with an underwater volcano. It makes the water near it warm. You can take a boat tour out there, though I did not have time to do that. Some think that the eruption of this volcano destroyed the civilization on the island, and that it was the site of Atlantis. It is a lovely island with striking contrasts between the buildings (mostly blazing white) and the rooftops, doors and shutters (mostly Greek blue).
I took a small-scale day “cruise” that went to three islands near Athens. Hydra, Poros, and Egina were the stops. I really enjoyed this trip, although the boat had seen better days (still safe, though). If your S and friend go on it, I recommend eating on one of the islands–even casual take-out type food, rather than the food on the boat. It was okay, but unlikely to appeal to college-age people. The people on the cruise will be very mixed in age and type, but your son and friend can wander the islands freely, in the time before they have to return to the boat. Hydra tends to be a favorite of most. Just the other day, I came across a T-shirt I bought that had the first lines of the Odyssey (in Greek), one of my favorite souvenirs.
If your S and friend like museums, then I recommend the Benaki and the Byzantine and Christian Museum, in addition to the Parthenon museum (which is a must for everyone, I think). My Greek friend took me to the Benaki, which I thought was one of the most interesting museums I have seen.
There is a bus tour around Athens (hop on/hop off type), which is useful for reaching some places of interest that are slightly far afield. Athens is very urbanized, and this tour is not as good as the similar ones in Rome or London, in my view. Still it is potentially worth taking to get an idea of modern-day Athens.