What "it was about a two or a three today" means in this context is, more explicitly, "The roughness of the sea today would rank with about two or three points on the sea state scale." Here is how we can come to that conclusion:
I have not seen the movie, but a quick Google search led to https://en.wikipedia.org/wiki/Sea_state, which describes the sea state scale. It is a scale from 0 to 9 describing the roughness of the sea using the height of the waves and swell as a measure.
With the knowledge from that article, we can understand that the phrase "a two or a three" is referring to the numbers on that scale. Because the person who asked the question mentioned the sea state scale in the question, the researcher is using that context as inferred when she gives her response. This means that she does not have to mention the sea state again, but the conversation's participants will understand that she is still talking about the sea state.
The article "a" is telling us that the words "two" and "three" are representing an object. In this context we can use inference again to understand that the object is actually the sea. So instead of saying "the sea was a two or a three," the researcher simply says "it was a two or a three."
So to tie all this information together, when the researcher is saying "a two," she means the sea was "a two", and "two" is referring to two points on the sea state scale.
This is much the same as saying "it was a dalmation", referring to a dog that was "a dalmatian". Similarly, one may refer to an earthquake measuring at 6.0 on the Richter scale in the same way, saying "it was a 6.0."