Wery hard to determine who is stronger.
Custodes are Emperor's guardians and bodyguards, that makes them one of the most powerful warriors in the Imperium. But to better perform their duty and in case of posible rebelion and/or influence on ane of then, Custodes dont fight as united force. In Aaron's Dembski Horus Heresy series book The First Heretic it's a scene where the Word Bearers astartes watch the fight of few Custodes. Wery quickly they see, that Custodes fight as individuals, not as a whole.
Thunder Warrior might not be as powerful as the Custodes, becouse they were not only mass produced but also issued with mass produced weapons and armours, jet they have the advantages of united combat doctrines and united fighting style, that makes them stronger than the invidual soldier in combat