After taking a second look at the option I was able to figure it out. Adding as an Internet password rather the a generic password and setting the protocol worked. Here is the working command:
sudo security add-internet-password -a "$EMAIL_USERNAME" -r "smb " -s "10.1.50.50" -w "$PASSWORD" -D "network password" -l "NY-File-Server" -T /System/Library/CoreServices/NetAuthAgent.app