I am 18 and haven't been sexually active for 3 years or so now. Over the past week, I noticed during masturbation a green bump (can move around, not really painful, same color as penis veins) under the head of my penis at the top of the shaft. I never remember this being so big/full until now, so any clue what this could be? It is about the size of one of those tiny chocolate chips.

Green sounds like it might be plain old pus in a boil or cyst.
If you had been sexually active, I might worry about trich, pronounced trick, short for trichomoniasis, a common protozoa infection that can be treated, but only by a prescription. The thing is though that's a STD.
So.. it can grow and get really disgusting when it pops. If you can get to a clinic, let them take care of it. Don't take the risk of infection moving in by popping it with a needle.
It's not really serious or an emergency.

Well the only girl I ever had sex with was tested for stds after we broke up and she had nothing..

Green sounds like it might be plain old pus in a boil or cyst.
If you had been sexually active, I might worry about trich, pronounced trick, short for trichomoniasis, a common protozoa infection that can be treated, but only by a prescription. The thing is though that's a STD.
So.. it can grow and get really disgusting when it pops. If you can get to a clinic, let them take care of it. Don't take the risk of infection moving in by popping it with a needle.
It's not really serious or an emergency.

Also it is under the skin. Does feel like it is sort of squishy, still kind of solid though.

Above skin or below, still probably plain old pus, very common.

Above skin or below, still probably plain old pus, very common.

Should I just let it go then? I don't want to try to pop something under the skin and freak out if I hurt myself

Read what I wrote above again.