Yes, 是 can be omitted in this sentence. However, the absence of the 是 means the tone of the sentence does not come across as insistent. What I mean by that is it sounds rather matter-of-fact and not so much like you're emphasizing that you really aren't watching TV.
In other words:
我在工作，我不在看电视。 = Yeah, I'm working. I'm not watching TV *shrug shoulders*
Whereas 我在工作，我不是在看电视。 = I am definitely working and definitely not watching TV.