Purpose: The absorbed dose estimation from Voxel-S-Value (VSV) method in heterogeneous media is suboptimal as VSVs are calculated in homogeneous media. The aim of this study is to develop and evaluate new VSV methods in order to enhance the accuracy of Y-90 microspheres absorbed dose estimation in liver, lungs, tumors and lung-liver interface regions. Methods: Ten patients with Y-90 microspheres SPECT/CT and PET/CT data, six of whom had additional Tc-99m-macroaggregated albumin SPECT/CT data, were analyzed from the Deep Blue Data Repository. Seven existing VSV methods along with three newly proposed VSV methods were evaluated: liver and lung kernel with center voxel scaling (LiLuCK), liver kernel with density correction and lung kernel with center voxel scaling (LiKDLuCK), liver kernel with center voxel scaling and lung kernel with density correction (LiCKLuKD). Monte Carlo (MC) results were regarded as the gold standard. Absolute absorbed dose errors (%AADE) of these methods for the liver, lungs, tumors, upper liver, and lower lungs were assessed. Results: Liver and tumor's median %AADE of all methods were <3% for three types of imaging data. In the lungs, however, three recently proposed VSV methods provided median %AADEs of less than 7%, whereas the differences exceeded 20% for existing methods that did not use a lung kernel. LiCKLuKD could achieve median %AADE <2% in the liver, upper liver and tumors, and median %AADE <7% in the lungs and lower lungs in three types of data. Conclusion: All methods are consistent with MC in the liver and tumors. Methods with tissue-specific kernel and effective correction achieve smaller errors in lungs. LiCKLuKD has comparable results with MC in absorbed dose estimation of Y-90 radioembolization for all target regions.