you may want to check with NY Waterway (http://www.nywaterway.com), as they have a ferry from near exchange place. (i was on one of the last trains to see that station open...)
that part of JC is decent at worst, in my humble opinion, but i don't get much trouble in Jersey City at all.
you also have NJTransit buses in that neck of the woods, which are an attractive option for the Wall Street routes. see
http://www.njtransit.com for more info there.