Chemistry - How was it concluded that the H3O+ rather than H+ is the "acid" ion?

Actually, the initial theories before Lewis suggested that $\ce{H+}$ is the cause of acidity. However, it soon turned up that an ion as small as the nucleus of hydrogen (you may simply call it a proton) can't be created in low energy reactions due to its high polarising power. So, $\ce{H+}$ is though the cause of acidic nature in aqueous solutions, $\ce{H+}$ never exists as $\ce{H+}$ but as $\ce{H3O+}$, $\ce{H9O4+}$, etc. It is because the proton is heavily hydrated. Though we are not very sure of what is the actual hydrated form, we usually refer it to as $\ce{H3O+}$ or $\ce{H+ (aq)}$.