The Best:
Bernard Haitink, London Symphony Orchestra live. Haitink's LSO recording of the 6th is a dramatic improvement over his earlier RCO recording on Phillips. Haitink's timpani are particularly effective in the storm (no holding back here). The sound quality is excellent too (though be aware that it was recorded from a live concert, and is a high density DSD recording, available in a hybrid SACD format). So, Haitink would be one of my top choice among digital era recordings; although be warned that it has some HIP elements, interpretatively, which may not be to all tastes:
https://www.prestoclassical.co.uk/classical/products/7944791--beethoven-symphonies-nos-2-6
https://www.amazon.com/Symphonies-N...U/ref=sr_1_6?s=music&ie=UTF8&qid=1513033477&sr=1-6&keywords=Haitink+beethoven+6
Fritz Reiner, Chicago Symphony Orchestra--this is a terrific performance, though I've heard better accounts of the 1st movement. For example, with Otto Klemperer you can hear the sound of chirping birds in the 1st movement more vividly than with Reiner--so that's a bit of a negative in my view. But, otherwise it's great, especially in the final movements, where the storm scene is truly terrifying in Reiner's hands! (and it needs to be if the country folks' "thanks" to the "Godhead" is to make any sense in the 5th movement). Good sound for its age.
Pablo Casals, Marlboro Festival Orchestra. Like Beethoven, Casals was a nature lover, and it really shows--his conducting of the 6th is near ideal. The older sound is good enough, though not for audiophiles.
Wilhelm Furtwangler, Stockholm Philharmonic--Furtwangler is also excellent in this symphony, but as usual he doesn't have great sound quality.
Carla Maria Giulini--with either the Los Angeles Philharmonic (1979) or New Philharmonia (1969) orchestras (I've not heard his final La Scala recording of the 6th):
Nicholas Harnoncourt, Chamber Orchestra of Europe. Harnoncourt is one of the best conductors in the 1st two movements, and especially in the 2nd movement: where he wisely opts not to take the movement so fast that he's unable to achieve a strong sense of tranquility and calmness, and yet he's fast enough that we can still clearly hear the sound of a babbling brook, i.e., moving water, as well. That combination is very tricky to pull off. Indeed Harnoncourt negotiates the two nature elements of this movement as well as, if not better than anyone. But frustratingly, he's not quite as strong as Reiner, Haitink & others in the final two movements:
The Very Good:
Eugen Jochum, London Symphony Orchestra
Bruno Walter, Columbia Symphony Orchestra--though Walter is too sentimental in the 2nd movement, in my view.
Erich Kleiber, Concertgebouw Orchestra of Amsterdam
The Best Performance on Period Instruments:
The only one I've liked was Frans Bruggen's first studio account for Phillips (though not so much his later live account):
Gardiner is overrated in the 6th, IMO, if you compare him to my above recommendations. For the most part, this symphony hasn't been a great outing for the period boys (Harnoncourt excepted, though the COE play on modern instruments), who are more successful elsewhere in the cycle (such as in the 1st, 2nd, 7th & 8th Symphonies, where they tend to shine).