Boson Sampling is a computational paradigm representing one of the most viable and pursued approaches to demonstrate the regime of quantum advantage. Recent results have demonstrated significant technological leaps in single-photon generation and detection, leading to progressively larger experimental instances of Boson Sampling experiments in different photonic systems. However, a crucial requirement for a fully-fledged platform solving this problem is the capability of implementing large scale interferometers, that must simultaneously exhibit low losses, high degree of reconfigurability and the realization of arbitrary transformations. In this work, we move a step forward in this direction by demonstrating the adoption of a novel compact and reconfigurable 3D-integrated platform for photonic Boson Sampling. We perform 3- and 4-photon experiments by using such platform, showing the possibility of programming the circuit to implement a large number of unitary transformations. These results show that such compact and highly-reconfigurable layout can be scaled up to experiments with larger number of photon and modes, and can provide a viable direction for hybrid computing with photonic processors.