Klinefelter Syndrome: This genetic condition is characterized by the presence of an extra X chromosome in males (47,XXY), leading to primary hypogonadism, which can cause delayed puberty, small testes, and gynaecomastia. The combination of these symptoms makes Klinefelter Syndrome a strong candidate for the single most likely diagnosis.

Hypogonadotropic Hypogonadism: This condition involves a deficiency in gonadotropin-releasing hormone (GnRH) or luteinizing hormone (LH) and follicle-stimulating hormone (FSH), leading to low testosterone levels, which can result in delayed puberty and small penis size. Gynaecomastia can occur due to an imbalance between estrogen and testosterone levels.
Androgen Insensitivity Syndrome (AIS): AIS is a condition where an individual has a Y chromosome and testes but is resistant to androgens (male hormones). This can lead to a range of phenotypes, from a female appearance to an undervirilized male appearance, which can include a small penis and gynaecomastia. However, the presence of gynaecomastia and the specific combination of symptoms might lean more towards other diagnoses.

Pituitary Tumors: Although less common, pituitary tumors can lead to hypogonadotropic hypogonadism by affecting the production of GnRH, LH, and FSH. Early detection is crucial as these tumors can be treated, and missing them could lead to significant morbidity.
Testicular Cancer: While testicular cancer itself might not directly cause delayed puberty, it can lead to hormonal imbalances, including elevated estrogen levels, potentially causing gynaecomastia. In cases of testicular cancer, especially in individuals with a history of undescended testes, early detection is vital.

Myotonic Dystrophy: This is a rare genetic disorder that can affect muscle tone and lead to hypogonadism, among other symptoms. While it's less likely to be the primary diagnosis for the given symptoms, it's a consideration in the differential diagnosis due to its potential to cause endocrine abnormalities.
Congenital Adrenal Hyperplasia (CAH): Certain forms of CAH can lead to an imbalance in sex hormone production, potentially causing gynaecomastia and other symptoms related to hormonal imbalances. However, CAH typically presents with other significant symptoms, making it less likely for the specific combination of delayed puberty, small penis, and gynaecomastia without other systemic signs.