Toll looks like 13.00+1.75 for #2, 5.00 for #3, 1.50 for #1 (all in the NY area, not sure about the rest of the trip). Discounts for E-Z Pass.

I think you can go entirely by highway on all 3 routes for very close to the same mileage so not I'm sure why you say that tilts you toward #3. For the same mileage I'd probably avoid NYC by doing #1 but you might prefer #2/3 for variety if you've never traveled them.

To clarify #3 you'd probably want to stay on 287 all the way to 95 (near the NYS-CT border), not using 87 at all (except where it runs together with 287). You can instead take 87 to 95 in the Bronx if you really want to but that's out of the way and does not have any obvious advantage.