The suit, the second $100 million claim she has filed in months, said the union did not protect her against bosses who harassed her because of her large breasts, the New York Post said.
She also claims she had been discriminated against for her national origin. Alyse's mother is from Nicaragua.
In March, the 29-year-old dancer with the touring company for Billy Joel's "Movin'Out" show sued choreographer Twyla Tharp and producers who allegedly criticized her breasts, which grew from C-cup to D-cup size, the New York Post said.
Alyse said she was humiliated, and even the costume designers were put out by having to alter her outfit to her changing proportions.
"Those (epithet) boobs are huge ... We hired you at a C, and now you're a D," she said the stage manager shouted, according to the Post.
Thursday's suit claimed the union had violated its grievance procedures by ignoring her, damaging her financially, emotionally and physically.
Joel was not named in either suit.