N.G.
It's so sweet that you are taking your role as Godmother seriously. I see so many people treat this role as such a meaningless tradition. The reason why my kids have no godparents is because I didn't know anybody who was willing to take it seriously and actually become a spiritual mentor for my children.
Gift ideas- perhaps new, age-appropriate bibles (toddler bible, preschooler bible, kid bible, etc.)? Also if I'm not mistaken, Precious moments has a series of statues that you could buy annually until you have the whole set for him- though that might be more appropriate for a girl. Perhaps framed scrapbook pages of his spiritual growth during that year that you could give to him each year, eventually to be combined into a book.