I think that it is too early to worry about an actual learning disability. It sounds like he is ahead in some areas, and behind that (to the extent of perhaps being merely average) in a few areas. In the end, I think that knowing number relationships is certainly important, but that other problem-solving abilities may be more important in developing higher math ability.
Using manipulatives sounds like it might help in the short term. In addition I have been using the IXL website off and on for my new five-year-old, and if I recall correctly in the pre-K and K levels especially, there are some skills where they have numbers next to pictures for simple addition, etc. Things like that might help your son.
I also think that the advice to work on his strengths is excellent. I would do more and more complicated word problems and logic puzzles. Those often don't depend on counting skills much anyway, and they will build your son's confidence. You may learn that your son has a high ability for general logical reasoning more than a math talent, but we don't all need to be mathematicians anyway.
