Tough call. Both of them really hamstrung by things other than their acting ability.
Cavill is a charisma vacuum in these films and these films alone. His character isn't superman at all, and some of the scenes and dialogue feel designed to make him unrelatable. Although man of steel is the best film with either of them in. He comes across as cold and uncaring, and I kinda hate the suit too. Then there's that moustache CGI face nonsense.
Affleck gives a decent performance, but again we never really get to see him be Batman. He's murderous, and doesn't really feel like a meticulous detective, or like he's using fear to intimidate, outside of a few scenes. He's in the least well written and directed films, and he even visibly gains and loses weight between scenes as he oscillates between dour humourless overly serious batman and goofy cracking wise Tony Stark wannabe.
I really dislike both versions of these characters, but I blame Snyder and the producers more than the actors, they're both capable actors.
Might go for Cavill being the better of the two because at least the Man Of Steel trailers hint at a far better version of that character that could have been possible.
Do we get a thread on whether Lois Lane or Amanda Waller is worse in the DCEU next?
Edit: I don't even mind that both of them kill, but it never felt earned or justified. If you are going to make them cross that line, it should be set up to be a big deal beforehand.
