The estimation of high dimensional quantum states is an important statistical problem arising in current quantum technology applications. A key example is the tomography of multiple ions states, employed in the validation of state preparation in ion trap experiments \cite{Haffner2005}. Since full tomography becomes unfeasible even for a small number of ions, there is a need to investigate lower dimensional statistical models which capture prior information about the state, and to devise estimation methods tailored to such models. In this paper we propose several new methods aimed at the efficient estimation of low rank states in multiple ions tomography. All methods consist in first computing the least squares estimator, followed by its truncation to an appropriately chosen smaller rank. The latter is done by setting eigenvalues below a certain "noise level" to zero, while keeping the rest unchanged, or normalising them appropriately. We show that (up to logarithmic factors in the space dimension) the mean square error of the resulting estimators scales as $r\cdot d/N$ where $r$ is the rank, $d=2^k$ is the dimension of the Hilbert space, and $N$ is the number of quantum samples. Furthermore we establish a lower bound for the asymptotic minimax risk which shows that the above scaling is optimal. The performance of the estimators is analysed in an extensive simulations study, with emphasis on the dependence on the state rank, and the number of measurement repetitions. We find that all estimators perform significantly better that the least squares, with the "physical estimator" (which is a bona fide density matrix) slightly outperforming the other estimators.