Coulomb crystals of cold trapped ions are a leading platform for the realization of quantum processors and quantum simulations and, in quantum metrology, for the construction of optical atomic clocks and for fundamental tests of the standard model. For these applications, it is not only essential to cool the ion crystal in all its degrees of freedom down to the quantum ground state but also to be able to determine its temperature with a high accuracy. However, when a large ground-state cooled crystal is interrogated for thermometry, complex many-body interactions take place, making it challenging to accurately estimate the temperature with established techniques. In this work, we present a new thermometry method tailored for ion crystals. The method is applicable to all normal modes of motion and does not suffer from a computational bottleneck when applied to large ion crystals. We test the temperature estimate with two experiments, namely with a one-dimensional linear chain of four ions and a two-dimensional crystal of 19 ions and verify the results, where possible, using other methods. The results show that the new method is an accurate and efficient tool for thermometry of ion crystals.