Sorry that you are away from your son more than you prefer. Everyone here assumes it's divorce, but for all we know you work on a nuclear sub or a marine biology platform away from home for months at a time. Either way, you deserve our sympathies for having to be separated, and you deserve our support for wanting to stay close to your boy.
For me it was divorce around when our son turned 3. We had (and still have) shared custody with him living with each of us on certain days. But for practical reasons, he's with his mom more, so the issue of how to stay connected was most important for me.
In my experience, a child that young has a tough time staying focused and connected to a voice on a phone. A voice alone is somewhat of an abstraction. As you surely know already, kids are really concrete. My son at that age found it difficult to stay focused and pay attention on the phone. If he held the phone himself, he was as fascinated by the buttons and the neat sounds they made when pressed as he was to talk to me (or to talk to my ex when he was with me). And if an iPhone with shiny screen buttons, even more distracting. If my ex held the phone near him on speaker phone, usually as he took his evening bath, he'd stray in and out of paying attention. It's just hard at that age.
I gave my ex my old MacBook so that we could do Skype and/or Facetime (when latter came along). That helped a good amount. Voice plus video is a lot better. Matters not whether it's an iPod Touch or iPad or laptop. Clear audio plus video equals better likelihood of paying attention and staying connected.
My son is 8 now. We still do the same arrangement, wherever he is, he calls the other parent and tries to do video chat every night. Neither of us has gotten him his own phone, and I think it will stay that way at least another couple years. He uses my ex'es iPhone or laptop to call me or he uses my iPhone or laptop to call her. I think it's better that we parents maintain control of devices and not let him have a phone for his own, at least so far. He'd be overjoyed to have a smartphone, no doubt about it, but we know that less phones and screens and more friends and outdoors and diverse activities is better.
I hope you find a way to make a good connection.