High speed rail can take the same grades as regular rail, so far as I know. And on the Water Level Route, there is no grade that gives any kind of problem to regular rail. So, it may not be flat, but it's not non-flat enough to be any kind of an obstacle.
Now, if you wanted to say that going up the Hudson clear to Albany before turning west - essentially, taking two sides of a right triangle instead of the hypotenuse - added too much distance for a serious high speed rail line, I could maybe listen to that. If you said that following the Hudson forced you into too many curves, which limited the speed, I could maybe listen to that. But the grades? No way. Not a problem.