We present a comprehensive set of spectral line maps of the molecular emission from Comets C/1996 B2 Hyakutake and C/1995 O1 Hale-Bopp, obtained with the Five College Radio Astronomy Observatory 14-m telescope. The comets were observed with the QUARRY focal plane array receiver, and the spectral line were assembled into a final data cube'' consisting of spectra at different positions within the coma. This final data set has a spatial resolution of approximately 80" and velocity resolution of approximately 0.1 km s-1. The HCN spectral lines in Comet Hyakutake during the near-perigee period revealed a systematic progression from asymmetric, single-peaked lines, to symmetric double-peaked lines. The median line velocity is blue-shifted approximately 0.1 km s-1, and the line width increases as expected with heliocentric distance. During the same time, the maps of the inner 20,000 km in the coma initially revealed strong, asymmetric emission, but evolved to weaker, azimuthally symmetric distributions. In Comet Hale-Bopp, which was observed over a greater span of time, the spectral lines were also generally asymmetric, or weakly double-peaked. The median line velocity was generally blueshifted, particularly at larger heliocentric distances, and the observed line widths are consistent with the outflow velocities derived by Biver {\it et al.} ({\it Earth, Moon & Planets}, 1998, in press). The emission maps reveal some asymmetries over the observed 200,000 km region.