I'd definitely try and get something in place to build his confidence...whatever interests him, or things that he has never even tried before, or even thought of, but which he can lose himself in, iyswim.
Off the top of my head, I'm assuming that he isn't sporty (might be very wrong, sorry if I am,) so maybe art, photography, something to do with wildlife/conservation..anything.
Would try and have his friends round, but you probably are doing all these things, anyway.
Again, might be wrong, but can you rule out bullying? Does he have access to social media? I can't think why a boy that age would be expressing such negative thoughts about himself unless he's had it said to his face/over the internet. Then again, don't have much experience of boys that age, so don't know why I'm even replying [blush.]
I'd try and get his dad to be a bit more involved, something regular that your son can count on if at all possible, although the distance might make that impossible.
Does his dad phone him, text him in between visits, or is contact only limited to when they can see each other? Could he and his dad do that thing where they play on the X-box together, even though they are miles apart. I imagine it would do him good to know that his dad genuinely would like to spend time with him, even if they are miles apart.