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The estimation of the direction of electromagnetic (EM) waves from a radio source using electrically short antennas is one of the challenging problems in the field of radio astronomy. In this paper we have developed an algorithm which performs better in direction and polarization estimations than the existing algorithms. Our proposed algorithm Snapshot Averaged Matrix Pencil Method (SAM) is a modification to the existing Matrix Pencil Method (MPM) based Direction of Arrival (DoA) algorithm. In general, MPM estimates DoA of the incoherent EM waves in the spectra using unitary transformations and least square method (LSM). Our proposed SAM modification is made in context to the proposed Space Electric and Magnetic Sensor (SEAMS) mission to study the radio universe below 16 MHz. SAM introduces a snapshot averaging method to improve the incoherent frequency estimation thereby improving the accuracy of DoA estimation. It can also detect polarization to differentiate between Right Hand Circular Polarlization (RHCP), Right Hand Elliptical Polarlization (RHEP), Left Hand Circular Polarlization (LHCP), Left Hand Elliptical Polarlization (LHEP) and Linear Polarlization (LP). This paper discusses the formalism of SAM and shows the initial results of a scaled version of a DoA experiment at a resonant frequency of ∼ 72 MHz. [ABSTRACT FROM AUTHOR]