Put this in your .bash_aliases or equivalent:

# Stop syncing a node_modules directory (via symlink)
noicloud() {
        mv node_modules node_modules.nosync
        ln -s node_modules.nosync/ node_modules
}
alias nocloud=noicloud

iCloud ignores files & folders with a .nosync extension, and also ignores symbolic links. This is the closest work-around I could find to prevent iCloud from having an endless recursive fit about it.