In this study, a parametric programming model was developed in order to deliver optimal management plans for various types of farms rearing endangered Greek sheep breeds under three distinct scenarios. The first scenario investigated the optimal internal organization of farms (i.e., management practices and resource allocation strategies that increase profitability of farms) under current market conditions (e.g., product prices) without, however, considering subsidies and compensations. The second assessed the impact of an agri-environmental support scheme on farm optimal structure and socioeconomic performance. The third investigated the effects of integrating farms into value chains and niche markets where premium prices prevail. For this purpose, a questionnaire survey was conducted in the wider region of Epirus and Thessaly, collecting management data from 16 farms rearing (i) Kalaritiko, (ii) Orino Epiru and (iii) Katsika rare sheep breeds. The main finding of this study was that the optimal internal organization of farms is essential for their self-reliance and viability. Therefore, it should be the basis in the designing of any initiative aimed at the preservation and valorization of local breeds. Furthermore, the analysis showed that a niche marketing strategy (i.e., a premium price strategy) can have a broader positive impact on farms structure and socioeconomic performance, particularly those engaged in cheese production, compared to an agri-environmental scheme. However, due to the fact that both initiatives possess limitations that may render them inefficient under specific external conditions, the development of an integrated incentive mechanism, which will combine both policy schemes and market-based initiatives, appeared to be a more effective strategy for the long-term viability of farms.