Primary Ovarian Insufficiency (POI): This condition is characterized by the loss of ovarian function before the age of 40, leading to infertility and irregular menses. The patient's symptoms of vaginal dryness, labial atrophy, and irregular menses, along with a history of Hashimoto thyroiditis (which can be associated with autoimmune ovarian failure), support this diagnosis. Elevated FSH levels, particularly in the context of low estrogen levels, are consistent with POI.

Polycystic Ovary Syndrome (PCOS): This is a common endocrine disorder among women of reproductive age, characterized by irregular menses, hyperandrogenism, and polycystic ovaries. While PCOS is a leading cause of infertility, the presence of vaginal dryness and labial atrophy might be less typical, as these symptoms more commonly suggest estrogen deficiency.
Hypothalamic Amenorrhea: This condition involves a lack of menstruation due to a problem with the hypothalamus, which can be caused by stress, weight loss, or excessive exercise. It could explain irregular menses but might not fully account for the degree of estrogen deficiency suggested by vaginal dryness and labial atrophy.
Thyroid Dysfunction: Although the patient's Hashimoto thyroiditis is reportedly controlled, uncontrolled or undertreated hypothyroidism can cause menstrual irregularities and infertility. However, the direct symptoms of estrogen deficiency point more towards an ovarian issue.

Pituitary Tumor: A tumor in the pituitary gland can disrupt the normal production of hormones that regulate menstruation and fertility, leading to symptoms similar to those presented. It's crucial to consider this diagnosis due to its potential impact on health if left untreated.
Premature Ovarian Failure due to Toxins or Infections: Exposure to certain toxins or infections can lead to premature ovarian failure. Identifying and addressing such causes is critical for management and potential prevention in other cases.

Turner Syndrome: Although typically diagnosed in childhood, some cases of Turner syndrome (a genetic disorder that affects females, causing short stature and lack of sexual development) might not be identified until adulthood, particularly if the patient has a mosaic pattern. However, this would be unusual given the patient's age and presentation.
Resistant Ovary Syndrome: A rare condition where the ovaries do not respond to FSH, leading to ovarian failure. It's a diagnosis of exclusion and would require further investigation.
Autoimmune Oophoritis: An autoimmune condition causing inflammation of the ovaries, which can lead to premature ovarian failure. This diagnosis would be considered if there were other signs of autoimmune disease and no other clear explanation for the ovarian failure.