Here is an old article that claims Gentian Violet is superior to nystatin:
NOTE: Nystatin can only treat the lumen of the intestine and won't treat the intestinal wall.
Nystatin (Mycostatin) treatment resulted in
dramatic reduction or disappearance of C. albi- cans from stools on culture, generally accom- panied by clinical improvement. However, as soon as the Mycostatin treatment was discontinued there was either a much increased growth or a reappearance of C. albicans in the stool cultures together with the return of the clinical signs and symptoms. One explanation of this phenomenon may be the fact that C. albicans can invade and parasitize the intestinal wall, as shown by Beemer, Pryce and Riddell.5 Myco- statin, because of its physico-chemical proper- ties,1would be unable to get into close contact with the fungus there and thus completely eradicate the causative organism in the gut.
Administration of Mycostatin, however, proved to be the most valuable procedure in corroborating the diagnosis and establishing the symptomatology of intestinal moniliasis.
So far, gentian violet seems to be the most useful therapeutic agent although clinical cure was secured in only a few cases. Cases of short duration seem to be more amenable to treat- ment than those of long standing.