My personal preference would be the I-86 route. I-90 is a bit shorter and probably a bit quicker, but you pay for it in tolls. I think I-88/I-86 is slightly more scenic, too, though neither is exceptional in that regard. I may also be a little biased from having traveled the thruway too many times going between home (Vermont) and college (RIT in Rochester). I-90 is a little more level than I-88 and I-86, which may be a consideration for a Toyota motorhome.
(If you take I-90 between I-87 and I-88 they don't charge you toll, even though it's otherwise on a toll road—going between those two exits is a special exception. Google maps doesn't seem to know that little factoid.)
Any of the three routes seems basically reasonable to me.