both methods are good. However, in plant in many case DNA reduplication occurred during early stage of cell differentiation without further cells division. In this case you cant use chromosome counting, so, only flow cytometry can give you data. Good luck!
Chromosome counting is a more confirmatory method and direct proof for ploidy level of any organism. Though Flow cytometry helps in determining the ploidy level but its peaks are based on the calibration of flowcytometer . It has to be standardized for the crop of interest or the crop for which flowcytometer was calibrated should have comparable nuclear DNA content to avoid biased inferences.
thank you for your useful replies, I used both method but the correlation between chromosome counting and morphological changes after ploidy induction had stronger R^2.