You can use vim programmatically with the option -c {command} :

Dos to Unix:

vim file.txt -c "set ff=unix" -c ":wq"

Unix to dos:

vim file.txt -c "set ff=dos" -c ":wq"

"set ff=unix/dos" means change fileformat (ff) of the file to Unix/DOS end of line format

":wq" means write file to disk and quit the editor (allowing to use the command in a loop)