I came across a book only last week aimed at children about life and death, 'Beginnings and Endings: with Lifetimes in Between' by Bryan Mellonie and Robert Ingpen. It's a Puffin book and the ISBN is 014-350144-5. At three, he might even be very ok with it, as long as you say the truth.
My GF's 3 year old dealt very well with the death of their dog just before last Christmas. They told him that the dog was sick and he was dead and not coming back. He nodded and never asked where the dog was after that, because he understood enough that he was gone forever.
I haven't had to deal with this when I have a child, it's hard enough trying to process it alone. I was devastated for months when my first horse was put down in 2000.