This can be easily achieved using your terminal
zip -r foo.zip foo -x "*.DS_Store"
Where:
a. -r for recursively including all directories underneath the targets we want to zip.
b. foo.zip is the name of the zip archive we are creating
c. foo is the target directory we want to zip up
d. -x “*.DS_Store” excludes all files whose path ends in the string “.DS_Store”