Unmanned Aerial System (UAS) is becoming a popular choice when acquiring fine spatial resolution images for precision agriculture applications. Compared to other remote sensing data collection platforms, UAS can acquire image data at relatively lower cost with finer spatial resolution with more flexible schedule. In recent years, multispectral sensors that can capture near infrared (NIR) and red edge spectral reflectance have been successfully integrated with UAS, and it is offering more versatility in soil and field analysis, crop monitoring, and plant health assessment. In this study, we aim to investigate the capability of UAS-based crop monitoring system to determine the best management practices for 3 different tomato varieties comparing different planting dates, plant density, use of plastic mulch and fertilization rate. The field and UAS data were acquired during Spring 2016, 2017, and 2018 located in Weslaco, TX. To compare the effect of various treatments in cropping systems, physiological parameters and vegetation indexes (Canopy Cover, Canopy Height, Canopy Volume and Excess Greenness) were extracted from red, green, blue (RGB) data and correlated with final yield data to evaluate practice/treatment to maximize tomato yield. During Spring 2016, we observed highest yield from the early March planting date using white plastic mulch. The results also indicated that the variety yielded higher presented a slow canopy decay towards the end of the season. In Spring 2017, there were differences in yield among the three tomato varieties depending on the fertilization rate, DRP-8551 performed better at low nitrogen level, Mykonos performed better on the two higher nitrogen rates and TAM-Hot-Ty had no significant difference among treatments. Finally, during Spring 2018, it was observed that early March produced the best yields and varieties that were able to slow canopy decay towards the end of season performed better. No significant difference was observed between plant density. It is expected that proposed system can be used to collect reliable data and develop variety and environment specific management practices to increase marketable yield and reduce production cost.