This source
http://civilwarintheeast.com/west-point-officers-in-the-civil-war/ shows year of graduation, class rank and which army they served in the ACW. If I counted correctly, there were three CSA Army officers with #1 class ranking: Benjamin Stoddart Ewell, class of 1829 (Robert E. Lee was #2 that year); Paul Octave Hebert in 1840; William Heny Chase Whiting in 1845. However, there is a question about Benjamin S. Ewell--his 1829 ranking appears to be an error--which means this is not my final answer--
my answer is in bold type below.
Benjamin S. Ewell (elder brother of Richard) was also shown on the list for 1832, where he was ranked #3. I spotted a couple other duplications of the #1 graduate (all Union) including James McPherson 2 years in a row as #1. I don't know if this means that Benjamin Ewell shouldn't have been #1 in 1829 (would that make RE Lee #1 that year?) or whether he did post-graduate work. No explanation was given in the article or any other place I could find.
This source:
http://www.civil-war.net/searchshsp2.asp?search=Graduates of West Point Serving in the CSA Army shows Benjamin S. Ewell #3 in the class of 1832. It still shows Robert E. Lee as #2 in the class of 1829. This source
http://www.americancivilwar.asn.au/meet/2002_10_mtg_westpt_classmates_enemies.pdf also shows Lee as #2 in his class.
This source shows Charles Mason as #1 in 1829, and states that he's most famous for being ranked ahead of Robert E. Lee. So
evidently my first source is in error!
That leaves only two CSA officers ranking #1 at West Point.
I'm sure there is a source somewhere that gives the exact number called for here, but I couldn't find it. I'm eagerly awaiting
@GELongstreet's answer and hope he has cited his source!
Bonus question:
DeWitt Clinton Baxter, Philadelphia PA
Sources: wikipedia articles, "DeWitt Clinton Baxter" and "72nd Pensylvania Infantry"
I couldn't find anything about him at Antietam other than that the 72nd PA was pushed back, but he fits the other criteria.