If you go for the oral suspension (liquid) - please ask for a compounded formula. Typical drugstore (premixed) Nystatin is loaded with sugar. You want the Sugar free version.
The difference between Fluconazole and Nystatin is that the Nystatin remains in the GI tract only, while Diflucan is more systemic and processed by the liver (which is also its downside). Most systemic would be Sporanox (Itraconazole).
All that said, I strongly recommend following Hv's advice regarding Candida overgrowth - supporting the adrenals (strengthening the immune system) while rebalancing your flora, correcting the terrain.