In control problems and basic scientific modeling, it is important to compare observations with dynamical simulations. For example, comparing two neural systems can shed light on the nature of emergent computations in the brain and deep neural networks. Recently, Ostrow et al. (2023) introduced Dynamical Similarity Analysis (DSA), a method to measure the similarity of two systems based on their recurrent dynamics rather than geometry or topology. However, DSA does not consider how inputs affect the dynamics, meaning that two similar systems, if driven differently, may be classified as different. Because real-world dynamical systems are rarely autonomous, it is important to account for the effects of input drive. To this end, we introduce a novel metric for comparing both intrinsic (recurrent) and input-driven dynamics, called InputDSA (iDSA). InputDSA extends the DSA framework by estimating and comparing both input and intrinsic dynamic operators using a variant of Dynamic Mode Decomposition with control (DMDc) based on subspace identification. We demonstrate that InputDSA can successfully compare partially observed, input-driven systems from noisy data. We show that when the true inputs are unknown, surrogate inputs can be substituted without a major deterioration in similarity estimates. We apply InputDSA on Recurrent Neural Networks (RNNs) trained with Deep Reinforcement Learning, identifying that high-performing networks are dynamically similar to one another, while low-performing networks are more diverse. Lastly, we apply InputDSA to neural data recorded from rats performing a cognitive task, demonstrating that it identifies a transition from input-driven evidence accumulation to intrinsically-driven decision-making. Our work demonstrates that InputDSA is a robust and efficient method for comparing intrinsic dynamics and the effect of external input on dynamical systems.