Direct and affectionate:
* Manco anch'io! (I miss you too!)
* Anch'io ti penso! (I think about you too!)
* Anche a me manchi! (I miss you too!)
Slightly more formal:
* Anche io ti penso molto. (I think about you a lot.)
* Anche a me manchi tanto. (I miss you so much.)
Playful:
* Non dirlo, mi fai venire nostalgia! (Don't say that, you make me nostalgic!)
* Anche io! Quando ci rivediamo? (Me too! When will we see each other again?)
If you want to express that you miss the other person a lot:
* Mi manchi tantissimo. (I miss you a lot.)
* Mi manchi da morire. (I miss you to death.)
Remember: The best reply will depend on your relationship with the person and the tone of their message.
You can also reply with a simple "Grazie" (Thank you) if you don't want to get too personal.