Traditional methods to measure spatio-temporal variations in above-ground biomass dynamics (AGBD) predominantly rely on the extraction of several vegetation-index features highly associated with AGBD variations through the phenological crop cycle. This work presents a comprehensive comparison between two different approaches for feature extraction for non-destructive biomass estimation using aerial multispectral imagery. The first method is called GFKuts, an approach that optimally labels the plot canopy based on a Gaussian mixture model, a Montecarlo-based K-means, and a guided image filtering for the extraction of canopy vegetation indices associated with biomass yield. The second method is based on a Graph-Based Data Fusion (GBF) approach that does not depend on calculating vegetation-index image reflectances. Both methods are experimentally tested and compared through rice growth stages: vegetative, reproductive, and ripening. Biomass estimation correlations are calculated and compared against an assembled ground-truth biomass measurements taken by destructive sampling. The proposed GBF-Sm-Bs approach outperformed competing methods by obtaining biomass estimation correlation of 0.995 with R2=0.991 and RMSE=45.358 g. This result increases the precision in the biomass estimation by around 62.43% compared to previous works.