They got Capone on tax evasion. He didn't think it was a minor thing.
I'm not sure that Heisenberg has evaded paying taxes.
When did he start earning drug money? The initial money was probably reported as gambling winnings. (Maybe he should file an amended return to clarify the source of those earnings, but I doubt there's a big penalty for misreporting the source as long as the taxes were paid.) As for the money he made after the gambling story, I'm not exactly sure of the timeline, but taxes aren't due on it until mid-April of the calendar year after it was earned. Are we there yet? (I guess he should have been making quarterly estimated payments, but the penalty for failing to do that is non-criminal.)
Also, I believe that burying cash in the desert is a deductible business loss.