I-86 is fine, maybe a little bit rough here and there (but not generally terrible as has sometimes been the case in years past), and of course not a toll road. Traffic is generally lighter on I-86 if that's a concern, though I-90 usually moves along pretty well, perhaps excepting rush hour times around Buffalo.
98 I'm not specifically familiar with, but it would be slower going than the Interstates. I would not expect any significant difficulties in general; usually numbered state routes are perfectly fine for RVs, though there are occasional exceptions. Taking the Thruway (I-90) would be the quicker route, I think.
Which way is better rather depends on what you desire in a route.
