I have a hard time decideing which boat was best, because they worked in different enviornments, and conditions.
U boats had it get progressivly harder on them, and had multiple nations working against them, also had technology from the allies get worse on them/ air power that made them caused alot of problems.
The us boats had it harder at the begining of the war. Faulty torpedos and other things made them have issues, but as the war went by things got somewhat easyer, and working conditions got better. Because the japanease wernt as advances as the allies when it comes to anti sub warfare.
So in my opinion nither sub was realy that much better than the other, there working conditions, and enviornments were different.
Things swhiched off, uboats got it harder, and fleet boats got it alittle easyer, and better technology.