Generally, I find ECM, MD&G, and Hyperion combine top notch recording with top notch ensembles in the chamber music area. Some specifics.
ECM
Schiff's recently completed cycle of the Beethoven Piano Sonatas. Watch out for vol 1 on the sonics but the rest are superb. Many will not like his Moonlight sonata though. (You may prefer the recently completed Ohlsson Cycle on Bridge. Volume 3 of the cycle is excellent, but that's the only one I've heard.)
Schiff and Perenyi on the Beethoven Cello sonatas is wonderful.
Levin and Kashkashian on the Brahms Viola Sonatas.
MGD- All of the Leipzig Quartet recordings of the Brahms Quartets are very good. Great performances coupled with a glorious warm sound. The op 18 Sextet coupled with the op 67 quartet would be a great disc to sample what the Leipzig offers.
Hyperion
The Floristan Trio may be the best chamber music ensemble I have ever heard. Try the Beethoven and Schubert piano trios first.
I also recommend the Leopold Trio/Hamelin Brahms piano quartets.
The Tackacs Quartet is now recording on Hyperion. Try The Schubert Death and the Maiden. Try also their Beethoven Late quartets on Decca.
Other suggestions. On the Shostakovich quartets, I strongly recommend the Quartuor Daniel on Fuga Libra over the Fitzwilliam set on Decca, which is good on the performance but woefully sup par on sonics. Also try the St. Lawrence Quartet Shostakovich 3,7,& 8. In my opinion, this exemplifies how Shostakovich should be performed.
I second the Bach Partitas by Hilary Hahn on Sony. Partita #3 Gets 3-4 plays a week in my house. It's that good!