My favorite is Musica Atiqua K”ln with Reinhardt Goebel (Archiv). The 3rd concert is unsurpassed. I think Goebel gave a gram of cocaine to each performer before playing it! The last movement is frantic!
My second choice would be the Leonhardt-Kuijkens version from Seon/Sony, from the early 70's. You can find in this version all the great names of the early historic-performance movement: Bylsma, Brggen, van Asperen... The recording is a bit bright, but the version is superb, very warm.
Then you have the version of La Petite Bande, with Sigiswald Kuijken.
A safe choice would be the classic version of Trevor Pinnock and the English Concert (Archiv).
Anyway, there are great versions out there, including those Andrew mentionned. You can't go wrong if you buy any of them. I wouldn't buy an italian version though (Giardino Armonico, etc). I think they are great playing Vivaldi, but not playing Bach. It's just my opinion though.