For those too lazy to click on the link here is the list of winners as suggested by Filichia. For several he doesn't pick a definitive winner so I listed his top choices. (If you want to see all of his reasons for each check out the actual article).
1947: Brigadoon
1948: High Button Shoes
1949: Where’s Charley
1950: Gentlemen Prefer Blondes
1951: Call Me Madam
1952: Make a Wish
1953: Two’s Company
1954: Me and Juliet
1955: The Pajama Game or Peter Pan.
1956: Damn Yankees
1957: My Fair Lady or L’il Abner
1958: New Girl in Town.
1959: Redhead
1960: Fiorello!
1961: Bye Bye Birdie
1962: How to Succeed
1963: A Funny Thing or Little Me
1964: Funny Girl
1965: Fiddler on the Roof or Half a Sixpence
1966: Mame
1967: Sherry!
1968: Darling of the Day
1969: 1776
1970: Purlie
1971: No, No, Nanette
1972: Follies
1973: A Little Night Music
1974: Raisin
1975: The Wiz
1976: A Chorus Line
1977: The Threepenny Opera
1978: On the 20th Century
1979: The Best Little Whorehouse in Texas.
1980: Sugar Babies or Oklahoma! or Evita
1981: Sophisticated Ladies
1982: Lena Horne "The Lady and her Music"
1983: Cats
1984: Sunday in the Park with George.
1985: Big River
1986: Big Deal.
1987: Les Miz
1988: Phantom of the Opera
1989: Jerome Robbins Broadway
1990: City of Angels
1991: Miss Saigon
1992: Crazy for You
1993: The Goodbye Girl
1994: Damn Yankees
1995: Sunset Boulevard
1996: A Funny Thing Happened...
1997: Chicago
1998: Ragtime
1999: Parade
2000: The Music Man
2001: The Producers
2002: Urinetown
2003: Hairspray
2004: Wicked
2005: The 25th Annual Putnam County Spelling Bee
2006: Tarzan and – yes – In My Life.
"You pile up enough tomorrows, and you'll find you are left with nothing but a lot of empty yesterdays. I don't know about you, but I'd like to make today worth remembering." --Harold Hill from The Music Man