Even if you buy into the whole notion of "representing geography", the problem is that state boundaries ceased to be representative of any meaningful kind of political distinction a long time ago, as evidenced by the massive red/blue splits in many states. It's not just NY - you can see the same thing in other large states, e.g. in WA where the split is geographical within state boundaries - west of the Cascades is very blue, east is very red. Nor is it unique to blue states - TX has the same exact issue with blue counties having a lot of population that is effectively not represented at all.

Unless and until this is fixed, there's no meaningful "geographic representation" in the Senate, so it's strictly a negative.