Computational fluid dynamics (CFD) simulations of complex fluid flows in energy systems are prohibitively expensive due to strong nonlinearities and multiscale-multiphysics interactions. In this work, we present a transformer-based modeling framework for prediction of fluid flows, and demonstrate it for high-pressure gas injection phenomena relevant to reciprocating engines. The approach employs a hierarchical Vision Transformer (SwinV2-UNet) architecture that processes multimodal flow datasets from multi-fidelity simulations. The model architecture is conditioned on auxiliary tokens explicitly encoding the data modality and time increment. Model performance is assessed on two different tasks: (1) spatiotemporal rollouts, where the model autoregressively predicts the flow state at future times; and (2) feature transformation, where the model infers unobserved fields/views from observed fields/views. We train separate models on multimodal datasets generated from in-house CFD simulations of argon jet injection into a nitrogen environment, encompassing multiple grid resolutions, turbulence models, and equations of state. The resulting data-driven models learn to generalize across resolutions and modalities, accurately forecasting the flow evolution and reconstructing missing flow-field information from limited views. This work demonstrates how large vision transformer-based models can be adapted to advance predictive modeling of complex fluid flow systems.