The best method to backup your database depends on what you have available to you. If you have ops manager, by all means, it is the best option.
If you don't have access to ops manager, mongodump is a great next choice. It will affect your performance, so be sure to do your dump on off hours.
Another option if you are using vmware is a veem backup of each node. This would allow you to upgrade each node one at a time and if you run into any issues, roll back the entire vm. If you aren't using vmare, this isn't an option at all.
The worst option is to backup the entire /data directory, it can be done, but I wouldn't recommend it. Especially once you upgrade and are using wired tiger as it's a bit more complicated to restore from a directory dump in my experience.
Overall, your question is asking for opinions. That is what my post is, opinions. I think the fact is, any backup is better than no backup and I'll leave it there.