We report a facile, room-temperature assembly of MoS2-based hetero-layered nanocrystals (NCs) containing embedded monolayers of imidazolium (Im), 1-butyl-3-methylimidazolium (BuMeIm), 2-phenylimidazolium, and 2-methylbenzimidazolium molecules. The NCs are readily formed in water solutions by self-organization of the negatively charged, chemically exfoliated 0.6 nm thick MoS2 sheets and corresponding cationic imidazole moieties. As evidenced by transmission electron microscopy, the obtained NCs are anisotropic in shape, with thickness varying in the range 5-20 nm and lateral dimensions of hundreds of nanometers. The NCs exhibit almost turbostratic stacking of the MoS2 sheets, though the local order is preserved in the orientation of the imidazolium molecules with respect to the sulfide sheets. The atomic structure of NCs with BuMeIm molecules was solved from powder X-ray diffraction data assisted by density functional theory calculations. The performed studies evidenced that the MoS2 sheets of the NCs are of the nonconventional 1T-MoS2 (metallically conducting) structure. The sheets' puckered outer surface is formed by the S atoms and the positioning of the BuMeIm molecules follows the sheet nanorelief. According to thermal analysis data, the presence of the BuMeIm cations significantly increases the stability of the 1T-MoS2 modification and raises the temperature for its transition to the conventional 2H-MoS2 (semiconductive) counterpart by similar to 70 degrees C as compared to pure 1T-MoS2 (similar to 100 degrees C). The stabilizing interaction energy between inorganic and organic layers was estimated as 21.7 kcal/mol from the calculated electron density distribution. The results suggest a potential for the design of few-layer electronic devices exploiting the charge transport properties of monolayer thin MoS2.