Yeah, it was Riku, for the reasons that AndyCloseEyes has already stated. Plus, Axel was already considered a traitor by the Organization, so he wasn't working for anyone but himself. Saix didn't show up until later. (Note how Axel seemed to feel guilty when Saix took Kairi. They weren't working together.) And the figure couldn't have been Axel, he had his hood off the entire time. Since Mickey's too small, Saix wasn't there, and no other Organization member would have bothered to look for Kairi at that point, that only leaves Riku.
Also, Kairi hadn't been kidnapped just yet. She left the island of her own free will; it wasn't until Axel dragged her away from Hayner, Pence and Olette that you could say she had been captured by anyone.