What could a small crater-like growth on my penis be? it has been there for years.

Any number of things: Growths on the skin, especially in the genital areas, can be from many different causes. Some are benign (non-serious) and others are more serious (warts, skin cancer, etc.) the only way to tell with certainty is to have this checked by your doctor.

See a dermatologist: It is very important to see a board certified dermatologist to have the lesion checked. Any new or non-healing lesions could represent an std, wart or skin cancer. There are also some benign lesions that can occur on the penis. Your lesion has been there for years and I am assuming it has not changed over this time period. Regardless, please have it checked to be safe.