First convert the binary files to .ped and .map if needed
http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml
then you can use gtool,
http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html
in particular, http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html#PED to GEN Conversion
gtool -P --ped example/example.ped --map example/example.map --og example/out.gen --os example/out.sample
Before this some awkward work need to be done