Can I disable logging 404 errors in my craft.log file?
Not currently, but I agree it's kind of annoying.

I thought maybe you could pull it off with a plugin since Yii does have an onException event, but there wouldn't be a way to disable logging of 404's without some code changes on our end.

I've added it to our 3.0 list to add a config setting to disable logging of 404's though.