Ahhhhh. For some reason I thought you were starting in Staten Island! But that's not at all what you wrote!

So yes, your original route (walk to Pier 79, NYC Ferry to BPC, walk to PATH, PATH to Newark Penn, Bus 62 to EWR) would work, but involves a good amount of walking and likely at least a couple steps on the bus.

A little less walking and I don't think any stairs, but a little more expensive and less regular schedule, would be to walk from Pier 88 to Pier 79, take the NY Waterway ferry to Hoboken/NJ Transit Terminal, NJ Transit to EWR (with a change at Secaucus), AirTrain to your terminal. Unless you're flying out of Terminal A--then you're going to also have a long-ish walk from the AirTrain to the terminal.

The least walking (without taking a cab or Uber/Lyft) would be M42 bus from the foot of Pier 83 (aka 12th Ave/42nd St) to the Port Authority Bus Terminal and then the Coach USA bus (that guv1976 mentioned) from Port Authority to EWR. I'm pretty sure the M42 is a flat floor bus and it shouldn't be crowded when you get on as 12th Ave is the first stop and you're only going a few stops.