The safest way would surely be a paper wallet, kept in multiple copies in safes and the like, that would be the safest method IMO, Another good way is a hardware wallet and keeping your coins protected.
Using a web wallet isn't the safest but something like blockchain and others which allow your access to your coins is acceptable IMO since the open-source code doesn't allow them access to your btc's and keys.
The best way to use the Paper Wallet is to talk to the computers recently when the virus is infected. I think the safest method is paper wallet. If possible, multiple copies must be made from the same paper. We have to share these with people we trust very much.