Conceptual approaches to research scientific methodology from general philosophical positions are summarized in the paper. The necessity of constructing ontologies for knowledge of modern reality is justified. Conceptual views about essence of ontology are considered and on this basis the general scheme for constructing economic ontology is proposed. By the author argued that the ontology is necessary prerequisite constructing and justification of scientific theory. Formation of the ontology allows representing scientific knowledge in the form of a theoretical scheme and thus makes it possible to identify regularities and the logic of scientific theory’s development. Economic ontology includes rationale and interpretation of theoretical concepts and categories and also allows to build a picture of economic reality, substantiating theoretical and methodological basis of economic processes research. Therefore to allocate their ontological components it is necessary to determine methodological foundations of economic concepts . In this connection methodological instruments ("hard core", the basic principles, the basic approach and methods of research, assumptions of analysis) of New Institutional Economics and neoinstitutionalism are demarcated by the author, as well as main differences between these two directions from neoclassical economic thought and "old" institutional economics are highlighted.