We are traveling from Bali back to the. US with a short stop in Kyoto and Tokyo. Is there somewhere to store 2 surfboards at the Tokyo airport?
I checked the links that uncovery provided and the limitation of baggage for "GPA" at the checked services is "1 linear meter" in size in any direction. Another site with different information notes that they only store up to 1.2 meters. So unless you have really short boards, you can't store them.
But if this link is to be believed, JAL-ABC does allow surfboards (no dimensional limit noted for Narita; under 2m for Haneda). The only problem is that I can't verify this as the links to JAL-ABC are broken from Narita's website. They might have gone out of business.
So the answer is a very conditional "maybe" -- and you should have a plan B in case you can't find any. Plan B might involve shipping your board from Narita to Kyoto, then posting it immediately back to Narita.