Anywhere east of the 78 loop (so downtown JC) is quite safe. The Heights is pretty safe for the most part. Journal Square statisically isn't too bad but it still gives me a rundown/dodgy feel. Bergen-Lafeyette is gentrifying rn so its block by block.

I would recommend downtown JC just due to accessebility to what you're looking for + safety + access to NYC.

How much luggage you have?

I would just try to get to Penn station and then catch the LIRR to Jamaica and air train from there. All together it's about an hour but it's semi comfortable if you don't have too many bags.

then move or get over it

Its horrid. Fuck paying for this horrible public transit service in the densest and most congested metro area in the US. It's a fucking embarrassment