I used to live in JC downtwon couple of years ago - there are a few good high rise apartments here but if you want to stay close to the waterfront, I would definitely recommend Gotham (no not Batman's city
) on the intersection of Warren and Montgomery as back when I lived I felt it was clean and secure. My rent was $2400 for a 2 bed 2 bath + utilities + $190 (garage). I would rate the Montgomery towers, right next to the Gotham next. Would stay away from Metropolitan towers as its roach infested. Further away there is Dixon Mills which is slightly cheaper than the ones I mentioned above and are good too.
I havent mentioned other apartments like Portside Towers as I feel they are ridiculously priced (~$3500 per month for a 2 bed) but if you are someone who loves views you might want to consider this along with Pier, Marbella, Liberty towers.
I dont really know if the situation has changed from back when I was there so dont come back yelling at me
good luck finding an apartment of your choice.
duh - didnt see the OP was that old.