▻ WHAT ARE WE LOOKING AT ?
☛ Methodological individualism (MI) usually indicates one of two views :
the main individualist claims usually hold either that theories referring to
social entities, social properties, etc. are in principle reducible to purely
individualist theories or that at least every social event, etc. can be fully
explained in purely individualist terms (Harold Kincaid, 'Eliminativism and
Methodological Individualism', Philosophy of Science, Vol. 57, No. 1 (Mar.,
If the term is to be used, I go along with JJC Smart's view that materialism is 'the theory that there is nothing in the world over and above those entities which are postulated by physics' (JJC Smart, 'Materialism', The Journal of Philosophy, Vol. 60, No. 22, 1963, 651). Other takes on materialism are available but this lightly extensional one seems to fit the phrase in the question, at least as far as concerns human beings, namely that we are just 'collections of molecules'. (We could be just collections of sub-atomic particles, of course, but let's stay with the questioner at the molecular level.)
▻ LOOK AT IT ONE WAY
MI as such makes no assumptions about the nature of the individuals to which social entities and the rest are reducible. It does assume that reduction stops at the level of human beings as interacting, conscious, purposive agents (and not of human beings as a 'collection of particles') but whether human beings are nothing but material objects, or some other kind of physical object, or minds-and-bodies is an issue with which MI is not concerned. MI is not inconsistent with materialism; as a methodology in the social sciences it takes no view on materialism.
Nothing I'm aware of in the work of von Mises, Boehm-Bawark, Menger or Rothbard assumes that MI - or methodological 'apriorism' as von Mises called it - assumes that we are nothing but 'collections of particles'. They were economists interested in the nature of social explanation, in human beings as (to repeat) interacting, conscious, purposive agents. If we are 'collections of particles' this was not the description under which they were interested in us any more than they were interested in our chemical composition as oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.
They could have accepted the identity theory that 'collections of molecules' are Locke's 'thinking matter' ('Essay Concerning Human Understanding', IV.iii.6) and that human beings are collections of molecules that are identical with interacting, conscious, purposive agents.
▻ LOOK AT IT ANOTHER WAY
On the materialist side only eliminative materialism : mental states (properties and events) are realised by physical states (properties and events) and a psychology of 'consciousness' and 'purposiveness' is replaceable by a purely physical account of human behaviour - would be inconsistent with MI as characterised above. Whether it would take a conscious, purposive human agent to produce such an account, I leave an open question.