It's so difficult to confidently recommend Beethoven cycles, as they all have their strengths and weaknesses (& besides, people have varying tastes and expectations). I actually find it more interesting to talk about the highlights (or disappointments) from the different cycles--such as Harnoncourt's 2nd and 6th, Chailly's 3rd, Hogwood's 1st and 4th, Gardiner's 7th & 9th, Immerseel's brilliant 7th!, Nelson's 8th!, etc. And, the various reasons why most of the period boys seem to fail so miserably in the 5th and 9th. Or, why the Eroica is so extremely difficult for most conductors to manage to pull off. But, if I were pressed to choose only a few cycles that offer the best combination of sound and performance, overall, I'd likely pick from the following sets:
1. On modern instruments: my choice would be between: (1) Bernard Haitink, Concertgebouw Orchestra of Amsterdam, Phillips digital (1989); (2) Eugen Jochum's newly remastered EMI set with the London Symphony Orchestra (in the Jochum ICON box set), and (3) Kurt Masur's 1st cycle with the Leipzig Gewandhaus Orchestra on the AMSI remasters from Universal Eloquence (which I slightly prefer to the Pentatone SACDs).
2. On period instruments: that's another tough choice, but it would be between (1) Frans Bruggen's 1st studio cycle on Phillips (which is better in both sound & performance from Bruggen's 2nd live cycle), (2) Gardiner's cycle on DG Archiv, and (3) Hogwood's set on L'Oiseau-Lyre. Granted, Gardiner is the only period conductor I've heard that has made a very good recording of the 9th (& Missa Solemnis), but I don't overly care for Gardiner's set otherwise (except for his 7th)--so I'd probably take Bruggen 1. Having said that, I certainly wouldn't want to be without Immerseel's 7th--which is one of my all-time favorite recordings of the 7th (as I thoroughly enjoy the sound of the original Viennese horns that Anima Eterna uses! which work perfectly with the original woodwinds & strings in this symphony).
3. HIP on modern instruments: another difficult choice: admittedly, I haven't heard all of Giovanni Antonini's recently completed cycle, including his 9th, but I'd probably lean towards John Nelson's cycle in Paris, as well Bernard Haitink's with the LSO live. Chailly's Leipzig set is good too, but it's too relentlessly driven when listened to in larger doses. Harnoncourt can also be good--such as his superb 2nd (& 6th), but he's more erratic in the other symphonies--as with his disappointing 4th & 5th. Charles MacKerras's set with the Scottish Chamber Orchestra has some exceptional qualities too, but it wouldn't be my first choice either. So, Nelson and Haitink are probably the most consistent overall. & Haitink is better in the 9th, which was one of the weak points of Nelson's cycle (i.e., the 4th choral movement).