What is the safest way to log MEW among of these?
1.Keystone File
2.Private Key
3.Connecting Metamask.
I think the best way is to use the keystone file. As much as you can, you should protect your private key. One way to protect it is to actually just keep it and hinder yourself from entering it to open your wallet, There are instances of fake websites that gathers private keys and transfer funds.