My DS is 5'10", 28 inch waist and get this...34 inch legs (he likes extra length in the legs because he also has large feet!).
Old Navy and American Eagle (both online) for jeans/khakis.
We buy the slim fit and they look really good. I wouldn't buy skinny-- imo they aren't flattering on tall, thin boys (or really anyone if you want the truth).
J. Crew factory has jeans/pants in 28 x 32-- but you usually have to buy online.