We present radiation transfer models of rotating young stellar objects (YSOs) with hotspots in their atmospheres, inner disk warps and other 3-D effects in the nearby circumstellar environment. Our models are based on the geometry expected from the magneto-accretion theory, where material moving inward in the disk flows along magnetic field lines to the star and creates stellar hotspots upon impact. Due to rotation of the star and magnetosphere, the disk is variably illuminated. We compare our model light curves to data from the Spitzer YSOVAR project (Morales-Calderon et al. 2014, Cody et al. 2014) to determine if these processes can explain the variability observed at optical and mid-infrared wavelengths in young stars. We focus on those variables exhibiting dipper behavior that may be periodic, quasi-periodic, or aperiodic. We find that the stellar hotspot size and temperature affects the optical and near-infrared light curves, while the shape and vertical extent of the inner disk warp affects the mid-IR light curve variations. Clumpy disk distributions with non-uniform fractal density structure produce more stochastic light curves. We conclude that the magneto-accretion theory is consistent with certain aspects of the multi-wavelength photometric variability exhibited by low-mass YSOs. More detailed modeling of individual sources can be used to better determine the stellar hotspot and inner disk geometries of particular sources.