Commuting advice?

I am going to maybe be getting a job within a few blocks of central park but am looking to live in NJ in Perth Amboy possibly to save money on COL.

My issue is that it seems like there are infinite ways to get from Perth Amboy to the Columbus circle station. which way would be the most cost effective? I`ve looked into paying the toll to take Tottenville all the way in but that's like $15 bucks a day and I'm assuming it would be both ways, this would also involve taking the ferry and finding parking in a limited area.

I've also seen routes on the NJCL all the way to penn station and transfer to a NYC line which seems like it would avoid the toll? I'm familiar with commuting into and out of DC but this seems like a whole nother level.