There are two possibilities here, but in a limited context. A lot of people recently asked why cannot 'to' be used in a given sentence, so have a look here for example.

But this is quite a simple "X is Y" sentence with both of them being noun phrases (and it doesn't matter that Y is negated), and it can be written in both ways: "X to (nie) Y", with both of them being in nominative; and "X (nie) jest Y", (Ser nie jest warzywem), with X in nominative and Y in instrumental.

So the option with 'jest' must be definitely accepted, but it looks differently grammatically.