This is a Federal prosecution, not state.
You misunderstand his point - he means that if Menendez were to resign or be expelled from the Senate, now he will be replaced by a Democrat appointee instead of a Republican appointee.
“now he will be replaced by a Democrat appointee instead of a Republican appointee.”
...but only until the end of his term - the 2018 election.
I think it more likely that they are going after him now to scuttle his re-election (because he is guilty, in their view).
This timing better serves the possibility of getting a Republican elected in NJ, by weakening the likely Dem candidate. A recent two term Governor (Chris Christie) is a relatively good option for a Statewide race. Having his opponent publicly dragged through the mud (including for a pattern of having sex with underage girls) might help his chances.