When a linear aromatic molecule within a nanogap is bound only to a source electrode, and an adjacent molecule is bound only to a drain electrode, the two molecules can interact via pi-pi stacking, which allows electrons to flow from the source to the drain, via pi-pi bonds. Here we investigate the thermoelectric properties of such junctions, using mono-thiol oligo-phenylene ethynylene (OPE3)-based molecules as a model system. For molecules which are para-connected to the electrodes, we show that the Seebeck coefficient is an oscillatory function of the length L of the pi-pi overlap region and exhibits large positive and negative values. This bi-thermoelectric behavior is a result of quantum interference within the junction, which behaves like a molecular-scale Mach-Zehnder interferometer. For junctions formed from molecular monolayers sandwiched between planar electrodes, this allows both hole-like and electron-like Seebeck coefficients to be realized, by careful control of electrode separation On the other hand for meta-connected molecules, the Seebeck coefficient is insensitive to L, which may be helpful in designing resilient junctions with more stable and predictable thermoelectric properties.