The emission nebula N66 is the brightest HII Region in the Small Magellanic Cloud (SMC), with the stellar association NGC 346 located in its center. The youthfulness of the region NGC 346/N66 is well documented by studies of the gas and dust emission, and the detection in the optical of a rich sample of pre-main sequence (PMS) stars, and in the mid- and far-IR of Young Stellar Objects (YSOs). However, there is a lack of a comprehensive study of this region in the near-IR that will bridge the previous surveys. We perform a photometric analysis on deep, seeing-limited near-IR VLT images of the region NGC 346/N66 and a nearby control field of the SMC in order to locate the centers of active high- and intermediate-mass star formation through the identification of near-IR bright objects as candidate stellar sources under formation. We use archived imaging data obtained with the high-resolution camera ISAAC at VLT of NGC 346/N66 and we construct the near-IR color-magnitude (CMD) and color-color diagrams (C-CD) of all detected sources. We investigate the nature of all stellar populations in the observed CMDs, and we identify all stellar sources that show significant near-IR excess emission in the observed C-CD. We select, thus, the best candidates for being young stellar sources. Results. Based on their near-IR colors we select 263 candidate young stellar sources. This sample comprises a variety of objects such as intermediate-mass PMS and Herbig Ae/Be stars and possibly massive YSOs, providing original near-IR colors for them. The spatial distribution of the selected candidate sources shows that they are located along the dusty filamentary structures of N66 seen in mid- and far-IR dust emission and agrees very well with that of previously detected candidate YSOs and PMS stars.