Shisui.

Ok, so since no one does 1v1 anyway that doesn't really matter, haha.

The reason why I think Shisui is stronger is that 2) he is easier to pair with other ninjas, 2) he has incredible synergy with Anbu Itachi which you should have already.

LM + Anbu Itachi + Iruka/Masked Man + Shisui is an incredibly strong team.

Jonin Minato on the other hand hasn't peaked yet as we don't have access to Madara [5 Kage Summit] nor bonds skill, which will cause his mystery to do insane damage.