For both of my daughter's they needed Nutramigen, a special formula for baby's with bovine protein allergies (even though they are not allergic to bovine proteins).
When it came time to transition (am actually in the process with my youngest now), I slowly started adding whole milk to the formula until it went from being formula to milk.
So for example my daughter drinks approximately 8 ounces. (She is on a special 100 cal formula so I have to measure out more scoops of formula than usual.). I start with 7 oz of formula & 1 oz of milk and do that for a day, then 6 oz formula & 2 oz of milk on day two. Somewhere in the middle I usually have to repeat a few days, however, within 2 weeks they are usually drinking whole milk.
Another thing that helps is if he has had other forms of liquid such as juice (cut with water if you don't want the sugar high). Going between numerous liquids will help him enjoy the variety and make it easier for you to give him the whole milk rather than the formula. (You could also try to give him fortified soy milk once a day, he might really like that).
Hope that helps :)