Both the routes you're considering are okay, in my estimation.
I-86 to I-88 has less traffic generally (particularly as you don't have to go through Scranton et al in eastern PA) and in my opinion is a bit more scenic. It has, in years past, had some pretty rough areas of pavement, but most of them, at least the worst bits, have been repaired in the last several years and it's not too terrible now.
I-80 on the whole is probably a bit better maintained, I-81 maybe a hair less so just because of the traffic it gets, and I-84 through PA and NY is miserably rough. Once in MA, I-84 is now fine although normally busy.