What [do you think] the best way [to master English] is? (natural, but casual)
What [do you think] is the best way [to master English]? (natural and proper)
With superfluous language removed: 'What is the best way?' or 'What is the best way to master English?'. This shows that the location of 'is' in your question makes sense.
Ending a sentence with a preposition is considered 'improper' by some people, and considered 'acceptable' by other people.
'What do you think the best way is?' (acceptable, casual)
'What do you think is the best way?' (more polite, proper)