Foucault notes that the human sciences are not sciences, but earlier in this passage, he also says that they do still belong to the realm of knowledge. The human sciences are simply other forms of knowledge, but certainly different from what we would call objective scientific (hard science) information:
They constitute, in their own form, side by side with the sciences and on the same archaeological ground, other configurations of knowledge.
Foucault's skepticism is justified because his overall project is to show how these sciences (i.e. biology, psychology, economics, philology) are contingent upon political and historical realities of a given time period. Simply put, our time and place influence the way we think. For example, democracy and capitalism are much more part of our modern thinking than they would have been for ancient Egypt. And these theories (democracy and capitalism) influence the way we think about all knowledge, including the human sciences.
This is where Foucault's term "episteme" comes in. It is similar to Thomas Kuhn's notion of "paradigm" which is a certain scientific worldview; these change over time when new knowledge is discovered, thus overturning or refuting old knowledge. Foucault's episteme is similar in that it refers to how the context of a specific historical time period conditions the way we think in all discourses; from the hard sciences to the human sciences.
In any given culture and at any given moment, there is always only one episteme that de-fines the conditions of possibility of all knowledge, whether expressed in a theory or silently invested in a practice.
To be sure, the episteme (historical worldview at a particular time) informs, conditions, and influences thinking in all disciplines. Think of the episteme as the world's (or a culture's) unconscious at a particular historical time. Foucault pays special attention to the human sciences to critique the ways that ideology (arising from the episteme) influences the way we think about economics, biology, psychology, and so on. He focuses on human sciences (rather than physics for example) because he is primarily engaging in a critique of how humans condition (create the possibilities and limits) their own ways of thinking. With the hard sciences, the object of study is objects: in physics, it is the electron, neutron, quark, etc. In the human sciences, the objects of study are human thoughts themselves: the way we think.
His "gripe" is more of a directed critique of ideas that we make ourselves. Physicists study objects; they don't make the quarks, electrons, etc. Foucault is studying the theories that we do create and how they arise from the episteme. In other words, in the human sciences, we create the things we study (structuralism, psychology, democracy); therefore, we have a responsibility to critique these theories we make because these theories influence all knowledge; from the hard sciences to the human sciences themselves.