A coated article includes a low emissivity (low-E) coating on a glass substrate. The low-E coating includes at least one infrared (IR) reflecting layer of a material such as silver, gold, or the like, and at least one high refractive index layer of or including NbBi. The high index layer (e.g., NBBiOx) is designed and deposited so as to be amorphous in the low-E coating, so as to better withstand optional heat treatment (HT) such as thermal tempering. The high index layer may be a transparent dielectric high index layer.