Median Income Aggregation

Hello folks, 

I'm working on a project where I'm trying to build a median income estimate for a larger, non-census defined area. We're essentially aggregating municipalities (county subdivisions), into a larger umbrella geography that is not defined by the census bureau (so not a county, msa or things like that). I am wary of using a PUMA to County Subdivision crosswalk because I am not quite sure how that would work with higher income municipalities next to lower-income ones.

Would anyone happen to know a good way of aggregating up to median income for this different kind of geography? Whether through an R script or some other tool? Would love any ideas on how to tackle this. 

Thanks, 

Peter