How are we defining best? Cultural impact? Overall plot relevance? Performance? Ability to overcome personal challenges?
Thor has no doubt had the biggest character arc. He has grown in each film he has been in. Gone from arrogant prince warrior to a rightful king. He also has lost the most. Lost his entire family, his home, his friends, his hammer, etc. Thor has had to dig deepest and grow into what he needs to be. In that regard, it's Thor. Cap, Iron man etc aren't even remotely close to overcoming what Thor has had to overcome. Growing out of who you are while losing everything that's dear to you, and becoming king of a realm of gods while being a saving grace for the people of earth is bigger and more personal of a growth than anything else in the MCU. Thor has had the most heroic triumph of everyone.
However, overall, it's gotta be Iron man. Because every little victory is a triumph. That's because of his pop culture influence, he is the hero who kick started all of this, and all to often, the plots revolve around him overcoming something.
So to rank the top 3 heroes of the MCU, I would go
Iron man
Thor
Cap