You're right, there aren't rivers connecting New England to areas to the south which hugely slows down any ichthyofauna movement. Maybe the last interglacial was equally depauperate for the same reasons, and the mountains would have been somewhat higher. Climate per se might not be the big barrier, since many species not found in New England live as far north as southern Ontario which if anything is colder than most of New England.

True, New Englands southern connectiveness was for a brief period during the beginning of the interglacial before sea levels rose.

I did remember a couple snippets from the last interglacial and it was a bit warmer if I remember right, accounting for pockets of tupelo trees and the rare shell of warmer water species washing up on shore. But whether this effected freshwater icthyofauna depends largely on the rate of warming and its effect on sealevel rise.

Western Vermont however has no excuse, it is (or was) an extension of the Saint Lawrence explaining its species difference.