We report the efficient aqueous dispersion of pristine HiPco single-walled carbon nanotubes (SWNTs) with ionic liquid (IL)-based surfactants 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), the thiolation of nanotube sidewalls with 2, and the controlled self-assembly of positively charged SWNT-1,2 composites on gold. Optical absorption spectra and resonance Raman (RR) data of obtained aqueous SWNT-1,2 dispersions are consistent with debundled and noncovalently functionalized nanotubes whose electronic properties have not been disturbed. Additionally, the dispersion of pristine nanotube material with surfactants 1 and 2 leads to a high degree of purification from carbonaceous particles. The chiralities of the 14 smallest semiconducting HiPco SWNTs in resonance with Raman excitation at 1064 nm (1.165 eV) were determined in SWNT-2 aqueous dispersion using UV-vis-NIR and RR spectra. X-ray photoelectron spectroscopy (XPS) and surface-enhanced resonance Raman scattering (SERRS) spectroscopy of SWNT-2 submonolayers on gold verified the encapsulation of individualized SWNTs with IL surfactants, the cleavage of S-S disulfide bonds formed in aqueous SWNT-2 suspensions, and the direct chemisorption of the SWNT-2 composite on bare gold via the Au-S bond. Aqueous dispersions of SWNTs with IL-based surfactants add biofunctionality to carbon nanotubes by imparting the positive surface charge necessary for interactions with cell membranes. Our technique, which purifies pristine nanotube material and produces water-soluble, positively charged nanotubes with pendent surface-active thiol groups, may also be translated to other carbon nanotubes and carbon nanostructures. Self-assembled, positively charged submonolayers of SWNTs can be further used for applications in cell biology and sensor technology.