The phrase not without color is an adverbial phrase. It is modifying pretended. The use of not without color means, in effect, with some degree of color.
Now for the sense of color. Here, I think the best fit definition is this one:
11. outward appearance or semblance; plausibility
In modern usage, the word pretend means to believe or assert something that you think is false. In the archaic use here, I believe it means to assert something, without any hint that you think it is false. I haven't found a reference to prove this.
Now, rephrasing the passage,
For, though this be confidently and somewhat plausibly asserted, yet I look upon a law as a notional thing...
(It sounds as if the passage is about whether the universe is under divine control. It allows that the idea of natural laws controlling things is plausible, while maintaining that there is something divine behind it all which freely follows those laws.)