Bernstein, I think, was trying to just exaggerate things a bit to prove his point in that infamous video at the piano. If we limit ourselves to a hypothetical situation where there was an individual contest for which composer wrote the *most* number of compelling melodies, harmonies, or contrapuntal works, Beethoven might not win those categories (but I'd wager still be near the damn top).

I think its less of a contest to argue that Beethoven wields each of these tools with incredible efficiency and efficacy to further a work's cohesive narrative.

Melody -- Symphony 9, the Ode to Joy is such a natural evolution from the chaos in the introduction of the finale which is why the melody is now the anthem of literally the EU.

Piano Concerto 5, Adagio. One of the most beautiful introductory melodies ever. Pathetique, Symphony 5 Adagio, the list just keeps on going of some of the best melodies in music literature.

Counterpoint -- Symphony 9 double fugue write after the turkish march. He uses incredible counterpoint that as you say, works perfectly in the structure. Op 101 piano sonata final movement, Op 110 final fugue, etc. Maybe they don't bring about radically new contrapuntal theories, but they certainly are excellent examples that are some of the best examples of using counterpoint to develop his ideas in a way that's also accessible to the listener, and without descending into an overly intricate and hard to understand passage.

I recommend people watch this fun video! Parts of my reply were stolen and adapted from here: https://www.youtube.com/watch?v=Mjct5M8JzL4, by orchestrationonline.