Why would my 5 year old son say he felt like there was "small glass" like pain on the underneath of his penis shaft?

Skin irritation. The underside of the penis can get a dermatitis, and become red and irritated. Have a look at it, and consider putting a little Hydrocortisone on it, and vaseline frequently through the day. Baking soda baths can also help, 2-3 times per week.