It is just an organic crab, but just how dangerous are giants if its as dangerous as one of em'? Plus, I think the hole connecting the fortress to the cavern is actually several Z-levels above the water and it has no wings or anything. Also, its during my first siege so if I could somehow capture it and sic it on the gobbos that would be particularly awesome dwarfy.
Well... you might want to send a whole bunch of dwarfs against it. Avoid going 1vs1 with these big monsters, try to overwhelm them instead with sheer number to exterminate them fast and with as few casualties as possible. In this case, if you can also manage to shoot bolts at it without allowing it to get its huge claws on an archer, you should be safe (this strategy works a lot well with beasts having ranged abilities: deadly dust, poisonous vapors, fire breathing, etc). If I understand the situation correctly, then indeed, only winged creatures could reach your fortress, and this isn't one of them. You seem to be a beginner, so your military might not be quite optimized yet, therefore, you should mentally prepare yourself for a few losses.
Sadly, FBs aren't affected by normal traps (unless you can somehow knock it out on top of a cage trap without killing it), so it could prove to be quite the difficult task.
But you could still survive the siege and release the goblin prisoners near said FB...