UPDATE: Because folks have reminded me of other Kojima relationships, I have decided to add some more options here. Let's go.
Friend #5 - The Weird One,
Nicolas Winding Refn
As many people pointed out, Refn and Kojima's appreciation for one another goes well beyond their products.
It seems they're so confortable around each other, Refn feels no need to wear pants.
And they like to do a fighting stance together.
No matter how many years pass by, this has never changed.
Friend #6 - The Traveling Companion, Mark Cerny
I can't believe I forgot Mark Cerny, Kojima's world tour buddy.
Cerny and Kojima have traveled around the globe together for work, but they didn't forget to have some fun.
In fact, Cerny may be his #1 drinking buddy.
And Cerny is very proud of friendship with Kojima.
CONCLUSION:
It's definitely hard to say. Geoff clearly loves him and Kojima clearly loves Mads. Del Toro seems to be with buddy from work and Reedus is the one he calls when he wants to kick someone's ass.
Though I have to say, it seems he is more interested in spending time with Mads recently.