In this work, functionalized carbon nanotubes (CNTs) using two polyamine polymers, polyethyleneimine (PEI) and polyamidoamine dendrimer (PAMAM), were investigated by thermal analysis in order to address preparation strategies to obtain low cytotoxic compounds with the ability to conjugate micro-RNAs and, at the same time, to transfect efficiently endothelial cells. Thermogravimetric analysis (TGA) was coupled to chemometrics as a novel analytical strategy to characterize functionalized CNTs from different preparation conditions. In particular, two starting materials were considered:very small CNTs and carboxylated CNTs (CNT-COOH) in order to examine the affinity with polymers. Chemometrics permitted to compare results from TGA and to investigate the effect of a number of factors affecting the synthesis of coated nanotubes including a different amount of involved polymer and the time required for the suspension for a satisfactory and reproducible preparation procedure. The results demonstrated the effectiveness of TGA as a tool able to address synthesis of coated CNTs to be employed as efficient drug delivery vectors in biomedical applications.