Being is the verb to-be, in -ing form.
You being the fish in the school play tonight made me laugh.
This is equivalent to
That you were the fish in the school play tonight made me laugh.
Note that you being does not have tense. The time has to be determined by the context and the speaker's intent.
You being the fish tonight at the school play will make me laugh
refers to future time.
You being the fish tonight at the school play makes me laugh
refers to the present.
In the above three examples, the time of you being comes from the tense of the main verb: made, will make, makes.
Now that the context is in the main question...
Leonard: Okay, so, she said she wants to slow things down. It’s like saying “I’m really enjoying this meal, I’m going to slow down and savour it.”
Howard: No, it’s like “this fish tastes bad, so I’m going to slow down and spit it out.”
Raj: You being the fish.
Leonard: I'm not the fish.
Here, Raj just makes it clear that Leonard is the fish in this analogy.
You being the fish = you are the fish
except that the present participle provides a sense of duration. That is, it can be represented as ~~~~~~~~~~~~~~. It also indicated limited duration, so Lenard being the fish lasts only as long as the analogy is at play, that is, as long as the guys talk about this subject.