Agroecosystem energy analysis is a useful tool for tracking some of the measures taken in the agricultural sector to mitigate greenhouse gas emissions in order to achieve the Paris Agreement climate targets. The objectives of this study were to (a) determine differences in energy inputs among tomato farming systems (greenhouse, open-field, and hydroponic), (b) group tomato farms according to energy productivity, energy efficiency, and carbon and blue water footprints, and (c) compare the carbon and blue water footprints of farming systems. Twenty farms (ten open-field and ten greenhouse farms) were selected via proportional stratified random sampling from the municipalities of Volvi and Lagkadas in northern Greece for study during 2015–2016, and one hydroponic farm (the “gold standard”) in the prefecture of Imathia in northern Greece was chosen for study during the same period. A combination of univariate and multivariate statistical methods was applied. Previously unrevealed similarities between farming systems were demonstrated by applying hierarchical cluster analysis (HCA) with energy productivity, energy efficiency, carbon footprint, and blue water footprint as variables. HCA indicated that seven of the ten greenhouse farms and the hydroponic farm were in the same cluster. The energy productivity and energy efficiency were highest for the hydroponic farm and statistically significantly higher in the greenhouse farms than in the open-field farms. The hydroponic farm had the smallest carbon footprint, while the greenhouse farms had the smallest blue water footprints. The greenhouses used statistically significantly less fuel, fertilizers, herbicides, stringing, and total energy than the open-field farms. The most important energy inputs were irrigation, fuel, and fertilizers for the open-field farms and greenhouses, and electricity and fertilizers for the hydroponic farm. Overall, the hydroponic system was found to be the most environmentally friendly. The above agrienvironmental indices may be useful to decision makers attempting to regulate the fragile balance between climate change and agricultural production.