I think if you go strictly by the number of clans, Grandfather Mountain by far has the most with well over 100 clans surrounding the field (perhaps as high as 140). To be honest I don't think anyone else comes close.
As for the size of the games and attendance there are several games that may be bigger. In that group that I know of would be: New Hampshire Highland Games (athletics and pipe bands bigger than GFM), Stone Mountain (fewer clans but lots going on), Long's Peak in Estes Park Colorado, and Pleasanton, California.
In this last group you are probably looking at 60-80 clans which is still pretty big. It all depends on what you are looking for.
There may be more big 3 day games, but these are the ones I have been to. You can usually find a list of clans in attendance at the website for any games if you are looking for a specific one.