William Flynn is hard to figure. Like my favorite designer, Colt, Flynn had a solid batting average with a portfolio of courses that are hard to beat for quality consistency. Unlike Colt, we have pretty accurately determined his contributions on various courses. I look forward to the same sort of research and discovery for Colt.
How does one consider courses that are NLE? Flynn's design for Boca Raton South would certainly be on many lists as might Mill Road Farm and Opa Locka. I don't doubt that BRS would be recognized as the best course in Florida and one of the best courses in America by many if it was still around today. It is hard to beat a course that is part Pine Valley and part Shinnecock (a later design influenced by Boca Raton South).
Ignoring Flynn's co-design work at Merion and TCC in Brookline, where a majority of the work is (Merion) or at one time was (TCC) Flynn and only considering his original designs, it is still hard to come up with a list limited to four courses. Without question, Shinnecock Hills would be on anyone's list. After that, there are plenty of candidates.