1) 저하고 같이 커피를 마실까요?
2) 저하고 커피를 같이 마실까요?
Which one is more natural & grammatically right?
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Both are all correct and natural.
Korean sentences have flexible word order. So those two sentences are grammatically correct.
And when saying in a conversation, some constituents or case paeticles can be left out in a sentence.
(저하고) 같이 커피(-를) 마실까요?
(저하고) 커피(-를) 같이 마실래요?
(우리가 함께/같이) 커피(-를) 마실래요?/마실까요?