Gravity's right: neither is better in an objective sense, it just depends on what you want to do with it.
I personally prefer the arbiter because:
*Intel seating = OSS + other goodies that I like more than command
*50% higher base turn rate
*less engineering seating (1 cmdr seat is enough for me, cmdr + lc is overkill)
*lc universal instead of ensign universal means more flexibility
*mastery gives resistance to kinetic damage, and in pve that's usually what'll kill you
5/3 weapons isn't that important to me since I'd run beam arrays on both.
The yamato get a hangar, an extra device slot, and slightly more base hull, but I don't think that outweighs anything above.