* Είναι ο Ιωάννης εκεί; (Eínai o Ioánnis ekeí?) This is a fairly literal translation. It's grammatically correct and generally understood. "Eínai" means "is," "o Ioánnis" means "John" (using the definite article "o" for masculine singular), and "ekeí" means "there."
* Είναι ο Γιάννης εκεί; (Eínai o Giánnis ekeí?) This is very similar to the above, but uses the more common diminutive form of John, "Giánnis."
* Μίλα με τον Ιωάννη/Γιάννη. (Míla me ton Ioánni/Giánni.) This translates to "Speak with John." It implies you want to talk to John, so it's appropriate if you're trying to reach him on the phone or through some other intermediary.
* Είναι ο Ιωάννης/Γιάννης; (Eínai o Ioánnis/Giánni;) This is shorter, simply "Is John?" It works if the context makes it clear you're asking about his presence.
Which one you use depends on the situation. For a general inquiry, the first two are best. If you're trying to connect with him through a phone call or other means, the third is better. The last option is suitable only if the context makes it clear you mean "Is John there?".