Is too OK here:
A: I’m going to NYC for work. And my friend is going with me.
B: You’re going to NYC to work and your friend is going too?
balboa1 B: You’re going to NYC to work and your friend is going too? The use of "too" is fine. I would put a comma after "work".
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balboa1B: You’re going to NYC to work and your friend is going too?
The use of "too" is fine. I would put a comma after "work". The question mark seems to be part of the sentence, which is probably not what you meant. Probably you meant the question mark to be part of "Is too OK here?"