Apple tree stunted growth
Apple tree is in distress as it stopped growing during the summer. Could this be cedar apple rust or another disease? Seems the outside of the tree is growing just fine but the leader is stressed.
Cheboygan County Michigan apple trees
I cannot see anything wrong with the leader, but it is obviously stunted compared to the other branches in the top of the tree.
You should remove it.It looks like it has been growing poorly for several years. Cut back to the branch that it is growing from with the real tight branch angle. That branch is the new leader and has passed the old leader. You can cut it now or wait until next spring. If you are going to make just the one cut now is fine. I would not recommend a lot of cutting now. I recommend against pruning in the fall from Labor Day until after Thanksgiving. When you remove the branch you might examine it to see if you see any dead areas on the bark or browning in the wood which would indicate an old injury.
It does look like the tree has had apple scab,
http://www.ipm.msu.edu/diseases/apple_scab, and spotted tentiform leaf miner http://www.ipm.msu.edu/insects/spotted_tentiform_leafminer.
From the looks of the leaves I would guess it is a Honeycrisp tree. The mottled yellowing of the leaves in Honeycrisp is normal. It is just something that Honeycrisp does.