The trouble is, there is NO best version. Many cycles have great strengths and insights and individuals' personal preferences will always play a part in the choice they make. I bet you any money you couldn't find any two people who would agree on their top 5 versions of Beethoven symphonies.
I agree with you about Bernstain not being a natural choice for Beethoven but I could never accuse any of his interpretations and being lukewarm.
Some versions of the Beethoven symphonies which are very highly regarded include (in no particular order):
Berlin Philharmonic/Herbert von Karajan (1960s series)
London Symphony Orchestra/Bernard Haitink
Zurich Tonhalle Orchestra/David Zinman (personally, I find this too fiddly and lightweight)
Chamber Orchestra of Europe/Nikolaus Harnoncourt
Scottish Chamber Orchestra/Philharmonia/Sir Charles Mackerras
Two versions I particularly like:
Berlin Philharmonic Orchestra/André Cluytens (late 1950s)
Cleveland Orchestra/Christoph von Dohnanyi
In addition to these, there is a classic version of Beethoven 5 and 7 one should always consider by the Vienna Philharmonic Orchestra with Carlos Kleiber.
Basically, however, you need to make your own choice about the version which suits you and what YOU want to get from the Beethoven symphonies.