It's not been said if the sword prevents him from genjutsu, so to those who are using that as a reason, no it's not a reason Kisame would win(and if it has been said that his sword stops genjutsu, then I don't remember reading it so link me to the chapter), because we have no clue, all we know is Kisame respected Itachi as a very strong ninja and wouldn't dare cross him. It's hard to say who'd win but due to the amount of respect Kisame had for him and the fact Kisame killed his friends and partners before and yet not Itachi kind of shows he might have feared dying against him as well. Just my thoughts
and to the guy way above who asked about if Kisame has the Samehade now, no Killer Bee is the current wielder. (Kisame got rejected by the samehade then later committed suicide