Well, Madara's chakra was equal to "most of" the Ten Tails. The chakra that Kaguya absorbed from the people trapped in the infinite Tsukuyomi was said to surpass the Ten Tails. In other words, her raw chakra reserves are more than double Madara's.
Beyond that, it all comes down to how effectively they use their powers. Neither of them seemed to use the level of attacks that they were capable of; Madara basically just used Limbo, Truth-Seeking Orbs, and Chibaku Tensei. Kaguya basically use Ash Bones, dimension-shifting, and super-powered Air Palms. They should each have been capable of using an absurd number of Bijuudama, or created godly chakra avatars. Madara could have created a Susano'o more powerful than Sasuke's Bijuu Susano'o, but simply didn't.
Frankly, Juubito seemed far more intimidating; Madara and Kaguya both seemed to downplay the amount of chakra they had at their disposal.
