Driving the shortest distance possible will reduce your total costs the most. It’s ~$40 daily driving costs from EB to Newark, for instance, before parking.

To WTC, you’d best be served trains going to Newark Penn Station, then PATH. From Newark Penn, it’s 25 mins by PATH to WTC, allow 30.

Buses ending at PABT need a 25 min A/C/E leg, trains ending at NY Penn need a 20 min A/C/E leg, walking included for both. It’s out of your way, but an option in case PATH to WTC has troubles.

On the bus side, there’s actually a CoachUSA aka Suburban Transit bus line #600 which goes direct from East Brunswick to downtown NYC, making stops along Varick and Broadway, including right at WTC. Here’s the current schedule: https://web.coachusa.com/CoachUsaAssets/files/99/route600.pdf

It is one of the lines leaving from Nielson Parking Plaza, and it also departs from the East Brunswick Transportation Center, if that’s closer. Both have $5 daily parking.

Trips are $13.20/one way, but if you’re going in 2-3x a week, the 20-trip multi ride bundle is $216 saving you $48. The total daily discounted amount is $21.60 round trip before parking. Travel time is 1h20m. That’s definitely the most seamless, but is dependent on tunnel traffic.

There’s also a peak hours/days bus option connecting to the PATH in JC; the NJT #68 goes up NJ 18, then arrives in JC about 45 minutes later at Grove St PATH. Then it’s a 7 minute ride to WTC. Schedule: https://content.njtransit.com/pdf/schedules/bus/68 Cost is $7.75, a 7 zone “intracommuter” ride. 20-trip bundles (poorly named “flex pass”) are $124. But then you have to add on PATH, at $2.75/one way or 20-trip $52, for a total of $17.60 round trip before parking. A bit quicker than CoachUSA, and cheaper, but with a connection.

On the train side, Jersey Ave is a great location, as others mentioned, for its frequency and express options. It’s $6/day in lot 3, or there are monthly $60 rates through ParkAmerica, worth it if you’re going 10x/month or more. It’s 1h10 total trip time on the NEC including transfer time at Newark, before driving time to/from Jersey Ave. That’s $9.75/one way and $156 20-trip flex, plus PATH as above for a total daily amount of $20.80 before parking. This one is best if there’s some massive accident on the roads, you live on the west side of EB, or you don’t like buses.

For flexibility, both CoachUSA 100/300/400/500 and NJTransit #138 serve PABT in Midtown, useful if you have work hours outside peak times.

Keep your eyes out for South Amboy’s ferry project, it would be about a 20 minute drive away from you. I’d expect a 40 minute ferry ride, definitely going to be a pricey contender though, but a nice occasional change of pace on a spring/summer day.

I highly recommend trying all these options a couple times at full one way price, just to see what fits your style. Note that with the buses, you’ll need to wave to them as they approach the stop to signal for a pickup, and that you need to push the stop button to request a stop.

Definitely don’t forget to register through your work for pretax transportation benefits, which can help you save additional money on both tickets and transit parking.