Functionalized Au and Ag nanoparticles (NPs) with ascorbic and tannic acid, respectively, were used as SERS substrates (SS). Several SS were fabricated with different loads of metal NPs deposited on silicon wafers. We focused on the thyroxine (T4) band at 1044 cm−1 and tracked its intensity and position at concentrations from 10 pM to 1 mM. For all SS, the band intensity decreased as the T4 concentration decreased. Additionally, the band shifted to larger wavenumbers as the NP loads increased. In the case of Au, the SS with the highest load of NPs, the minimum concentration detected was 1 μM. The same load of the Ag NP SS showed a better performance detecting a concentration of 10 pM, an outcome from a SERS-EF of 109. The NP spatial distribution includes mainly isolated NPs, quasi-spherical clusters, and semi-linear arrays of NPs in random orientations. From the numerical simulations, we conclude that the hot spots at the interparticle gaps in a linear array of three NPs are the most intense. The Ag NP SS demonstrated good sensitivity, to allow the detection of pM concentrations. Therefore, its complementation to any immunoassay technique provides an interesting alternative for point-of-care implementations, such as test strips.