I would like to visit NY in future if you are also there.
Is this a correct sentence? I am concerned about the "are" part.
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I'd guess that what you are trying to say is that you would like to visit NY, if at the time that you visit the other person will also be there. If so, what you should say is, "I would like to visit NY in the future, if you will also be there."
The sentence you have written is grammatically valid (except that you should say "the future", not just "future", but that's not your question). But it doesn't make much logical sense. Taken literally, it means, "I would like to visit NY in the future, if you are in New York now." It's possible that you mean that, but unlikely.
It would make perfect sense to use this combination of tenses in other cases. Like, "I would like to buy a model XYZ cell phone in the future, if you have one." That is, if you have one now, I would like to buy one some day.
Is your friend in New York already and you plan to meet him there?
Or are you planning to visit New York and you are asking your friend to visit the city with you?
In the first case, say:
"I would like to visit New York in the future if you are there."
In the second case, say:
"I would like to visit New York in the future if you will go with me."