I think about this all the time. I've always felt that 2005 is one of the best groups. Anyone of those shows could have won Best Musical in another year, and each of them could conceivably be revived on Broadway. It was also a pretty evenly distributed Tony Awards - each of these shows won 1 acting award, and they almost evenly split Musical/Director/Score/Book (Scoundrels came up short, with Spamalot taking both Musical and Director).
There are very few that I would say were truly great "top to bottom," but I would include in the mix years where all but one were great. Strongly agree with 1991, and echo others with 1957, 1960, 1963, 1964, 1976, 1998, 2004, 2006, and 2017. If I had to pick 5 nominees, it would be:
1964 (Hello Dolly, Funny Girl, She Loves Me, High Spirits)
1991 (Once on This Island, The Secret Garden, Miss Saigon, The Will Rogers Follies)
1998 (Lion King, Ragtime, Side Show, Scarlet Pimpernel)
2005 (Spamalot, Spelling Bee, Dirty Rotten Scoundrels, Light in the Piazza)
2017 (Dear Evan Hansen, Come From Away, Groundhog Day and Great Comet)