Having some conflicting thoughts... post your opinion?

I've worked as an intern for a security consultant who does pentesting and I'm really learning alot. A typical day:

I show up at work around 8:00. We talk about what he hacked last night, if I have questions then he answers them. We will log into our computers. He will work on a project or something personal while I either do his documentation or just hang. I usually practice the command line.
We do this until lunch. We go to lunch, he pays for both of us,
and we go back to the office. We go back to work, usually he is showing me his tricks and giving me material to read. At 4 I go home.

The problem is... When I got my first paycheck it was very strange. We were at lunch and he asked me if $100 was okay for 3 weeks of work. I said no, and he gave me $200.

I mean I know I am learning alot from this guy and he does alot for me but is this right? I know it probably isn't even legal but I do more learning than work, what should I do? I don't want to risk my job or get him in trouble

You're an intern and you're getting paid? Many interns don't get paid at all. It's perfectly legal. An internship is generally exempt from laws regarding wages. It's not really considered a job. It's considered part of your education, like attending school.

Stay for awhile and learn the job. Later on, you can always negotiate money depending on what you know and if there is plenty of work and he needs you. You can also take those skills to another place. If he's paying you under the table, even better. Think of your resume and where you want to go with this.

Be advised that most interns don't get paid anyway so consider yourself lucky
An internship is just to get HANDS ON EXPERIENCE...
I am a Certified Medical Assistant none of us got paid to do our internships, we just got the option to work at the place we did our internship once we graduated

well you said he does alot for you? This kinda makes it different than a normal job. You are learning from him, now if you were being fully productive and dedicated im sure that you would earn more. If you have a problem ask him.

It isn't right that he is paying you low , but it is illegal. However, he's paying for lunch which can save a lot of money.

I don't have an answer for you but I do have a question:

What in the HECK was the agreement regarding your compensation?!?

You should get more than 200.