Well, here is a round up of the versions I have:
Karajan 1963: Generally viewed to be his best. It certainly has the best sound, recorded in the Jesus-Christus-Kirche, which has a great acoustic. His soloists are (probably) the best assembled for such a recording. Compared to his 1977 release, I find this one very cold. It is not hard to see the smoothness-obsessed Karajan of the '70s and '80s appear in ths recording. However, it is better than many other recordings and is not without its charm.
Karajan 1977: I prefer this one. It was done in the Neue Philharmonie, which has a boomy acoustic. However, the orchestra plays with feeling. His soloists here are almost as good as the '63 crew (Peter Schreier is probably better). This was in the middle of his "smoothness" fetish, but doesn't suffer horribly. Avoid the SACD if possible. It has a veil that the original Galleria CD doesn't, and even the Karajan Collection release sounds better.
Karajan 1984: The less said the better. This was smack in the middle of Karajan's digitization mania. The orchestra and soloists are a bit less-than-fantastic. The early digital sound is OK, but glassy in an extreme. It's also a bit hard to find in a single release. I bought it to complete my Karajan DG set of 9ths. I don't regret buying it, but it is not my favorite by a long shot. Most reviewers are inclined to dismiss this one as later Karajan trying to increase his catalog.
Furtwangler 1937: The Covent Garden recording is in a bad way. However, there are those who felt that this was Furtwangler's greatest performance of the work. There is a mysticism here that, while constant throughout his recordings, is in full swing. This is the communal Furtwangler 9th of legend. That is apparent even through bad sound. This is as close as we can get to the 9th that made Furtwangler famous.
Furtwangler 1942: This is the legendary Berlin 9th, recorded live during the war. It is famous for its intensity and drive. The recorded sound is not ideal, but it doesn't matter. The orchestra, chorus, and soloists give it their all. Such intensity should be sampled rarely, lest it lose its edge. The source tapes are clearly overloaded at times, and the recording is - at times - very poorly done. One does not get the impression that it was intended to be archived. Of course, one can never predict performances like this. Who can time perfection?
Furtwangler 1951: Recorded at the reopening of the de-Nazified Bayreuth Festival in 1951. Probably has the best sound of the lot of Furtwangler 9ths. It is brilliant in its jubilation. This performance is wonderful on so many levels. One sees the mysticism of prewar Furtwangler collide with the intensity of the war. The results are fantastic. One senses that this is as much about Furtwangler as Beethoven. His postwar tribulation is famous. The fact that he, not rival Herbert von Karajan, was called upon to reopen the jewel of German culture was no small vindication for the aging maestro.
Furtwangler 1954: Recorded in Bayreuth, at the opening of the '54 Festival. The sound isn't good. This was recorded a few days before the famous Lucerne performance. It is late Furtwangler. The '51 style has matured, and seems to have become a bit more introspective. Of course, his death was largely a loss of will to live (according to the doctors, he was going to recover from his pneumonia), so there was certainly much introspection during his last months. Very good. It's worth it to have Windgassen singing the 9th.
Gardiner '94: The dean of period Beethoven in Beethoven's masterpiece. Well-sung and well-played. This is a great 9th, period or not. It is blindingly fast, which might be a problem. Gardiner doesn't fool around. The orchestra is in good form and the soloists are in good voice. Through his tempi, Gardiner manages to create and release a tension that I find necessary for the work over the length of the recording. It is a part of his '94 set.
Bernstein '89: Recorded in 1989, after the fall of the Berlin Wall. It is a multinational conglomerate orchestra. The soloists are alright, and there is a sense of occasion. However, Bernstein adopts plodding tempi. The last movement is almost half an hour long. Compare that to the usual 25 minutes. I don't think he taking more repeats. It just seems slow. That's fine; however, it is dangerous to confuse ponderous tempi with great drama and tension. James Levine found out, at about the same time in his MET Das Rheingold, that being slow does not mean that one is being momentous.
Except for the '84 Karajan release, a case could be made for each that each is the best. I am partial to Furtwangler's '42 or '51 recordings. The '54 is up there, though. As far as I can tell, each cutting has its partisans. It is really up to the person diving in to decide what they want and who comes closest. I cannot think of a 9th without some merit; however, in a work as staggeringly brilliant as this, some merit doesn't cut it.