Mediocre/Poor letter of rec from well-known professor vs great letter from not as well-known professor?
Always go for the recommendation from the professor who knows you better. A letter from Albert Einstein that goes "mayradio0508 was never late to class and has nice handwriting" will not carry any weight.

Having said that, it sounds like you underestimate what this professor will be able to say about you. Running simulations and writing programs to handle data is something you do in research! The professor has also said you did a good job, which is a good sign. Besides, of the other three options you mention, it sounds like none of them can comment on your research ability (the third one can, but you've not started doing research with him).

If you're concerned he won't be able to say something good about you, you could always ask him: "Prof so-and-so, will you be able to write me a strong recommendation letter?"