Template-free controlled aggregation and spectral properties in fluorescent organic nanoparticles (FONs) is highly desirable for various applications. Herein, we report a nontemplated method for controlling the aggregation in near-infrared (NIR) cyanine-based nanoparticles derived from a group of uniform materials based on organic salts (GUMBOS). Cationic heptamethine cyanine dye 1,1',3,3,3',3'-hexamethylindotricarbocyanine (HMT) was coupled with five different anions, viz., [NTf2-], [BETI-], [TFPB-], [AOT(-)], and [TFP4B(-)], by an ion-exchange method to obtain the respective GUMBOS. The nanoGUMBOS obtained via a reprecipitation method were primarily amorphous and spherical (30-100 nm) as suggested by selected area electron diffraction (SAED) and transmission electron microscopy (TEM). The formation of tunable self-assemblies within the nanoGUMBOS was characterized using absorption and fluorescence spectroscopy in conjunction with molecular dynamics simulations. Counterion-controlled spectral properties observed in the nanoGUMBOS were attributed to variations in J/H ratios with different anions. Association with the [AOT(-)] anion afforded predominant J aggregation enabling the highest fluorescence intensity, whereas [TFP4B(-)] disabled the fluorescence due to predominant H aggregation in the nanoparticles. Analyses of the stacking angle of the cations based on molecular dynamic simulation results in [HMT][NTf2], [HMT][BETI], and [HMT][AOT] dispersed in water and a visual analysis of the representative simulation snapshots also imply that the type of aggregation was controlled through the counterion associated with the dye cation.