The Spain boss believes his compatriot has often been unfairly scrutinised this season after replacing the treble-winning coach at the Allianz Arena last summer
The Bavarians stormed to an historic treble of Bundesliga, DFB-Pokal and Champions League titles under Heynckes last season before Guardiola replaced the German trainer during the summer of 2013.
The former Barcelona boss has already lifted the Uefa Super Cup and Club World Cup this term and is firmly on course to defend last season's trophies, yet question marks have still been raised as to whether the team has truly improved under Guardiola - something which Del Bosque feels is unfair.
"I find these comparisons disrespectful," he told Bild. "What does it bring them? Jupp and Pep are great coaches.
"The Bayern of Jupp won everything and they loved him. But what Pep can and could do in every game proves not to be enough. But I'm a fan of both of them."
Bayern secured a 2-0 win away to Arsenal in the Champions League last 16 first leg on Wednesday and Del Bosque suggested only the three Spanish teams in the competition will be able to stop the Bavarians retaining their crown.
"They play wonderfully. The game in London was once again a tactical feat. The [Wojciech Szczesny] sending off of course dealt them the cards, but we saw the class within the team and of course the coach," he continued.
"[They are] a big favourite, of course. They are the main competitor for the three Spanish teams. Real Madrid, Barcelona and Atletico [Madrid] are in good phases and are difficult for any opponent.
"But Bayern are a very, very great team, without a doubt. It's really fun to watch them."
Bayern are currently 16 points clear at the top of the Bundesliga and have yet to lose a league this season, and Del Bosque freel admits that he thought last season's runners-up Borussia Dortmund would have put up more of a fight in the title race.
"You would perhaps have expected a bit more resistance from Borussia Dortmund. After they played such fantastic football in Europe last year, you would think that they would compete better in the league. But Bayern are just so hard to beat," he added.