Well that depends on if you are a pilot. The "in which we flew" in the first sentence, would be what a passenger would say. If you were a pilot flying the plane, you flew the plane. So, if you mean to say that as a passenger you were comfortable, Sentence 1 is correct. If you meant to say that you were one of the pilots flying the plane, Sentence 2 is correct.

If you are writing an academic paper, never end a clause or sentence with a preposition (i.e. "the plane which we flew in"). However, in conversation, go with whatever flows and is less clumsy.

I think both 1and 2 are right,

I think 1is correct.

1 is correct