Every individual has different size nipples. It may be that your nipples have grown slightly faster than pectoral (chest) muscles have. Eventually as you grow and begin to develop large chest muscles your nipple size will even out. It is possible that it may be a portion of your muscle below your nipple that is increasing in size, especially if you lift weights or are physically active, but it is hard to be certain.
What you are feeling beneath your nipple may actually be breast tissue. Gynecomastia is breast development in male teenagers. It is a completely normal part of adolescent development and disappears in 85% of young men within two years. Sometimes, especially if it is particularly bothersome, plastic surgery can be helpful.
If you feel that your nipples are abnormally large, that there may be something like a growth that could be causing them to be large or you are just uncomfortable do not hesitate to see your doctor. He/She would be able to inform you if it is a muscle causing this rising beneath the skin and also what other options are safe in order to correct it. It may all be simply a matter of time and growth before your nipples are at their correct size.