Pulse shape discrimination in scintillators is one of the most popular ways of recognizing events due to neutrons or gamma rays. Presently, n-γ discrimination is done mainly using two methods, charge comparison or zero-crossing. The aim of the study is to compare digital implementation of both algorithms using the same experimental data. For this purpose special application was developed in LabView environment which analyze the data digitized by Tektronix oscilloscope TDS5104B. The software allows optimization of each algorithm depending on the properties of the recorded pulse. The comparison is based on values of Figure of Merit and their relation to the light pulse characteristics. Both methods are used in measurements with XP5500B photomultiplier and Stilbene scintillator. Additionally the analysis of the detectors based on two types of Hamamatsu silicon photomultipliers (12×12mm2 and 24×24mm2) is presented. The results are compared with an analog zero-crossing system based on NDE202 NIM module.