The central midfielder was not included on the shortlist which was announced by the Premier Soccer League (PSL) on Monday.
Mamelodi Sundowns duo of Percy Tau and Hlompho Kekana‚ and Maritzburg United utility player Siphesihle Ndlovu are the three nominees for the accolade.
However, Larsen has insisted that Nyatama, who had a good season with Pirates, should have also been on the list.
“I think this is the best I’ve seen Musa Nyatama playing. When I had him at Bloem Celtic‚ I never saw him scoring a goal with his head but suddenly he’s scoring with his head," Larsen said on TimesLive.
The 30-year-old joined the Buccaneers from Bloemfontein Celtic prior to the 2017/18 season and he established himself as one of the team's key players.
“I don’t know what coach Rulani and Micho (Milutin Sredojevic) did to him but he’s chipped in with some important goals this season. I just think the role he plays within his team (Pirates) … that deep lying midfield position‚ he excelled in that role and has been the heartbeat of his team," he continued.
“I was very impressed with the season that Nyatama had. For me‚ Percy Tau and Musa Nyatama are the two players that gave standout performances throughout the season," he concluded.
Nyatama helped Bucs qualify for next season's Caf Champions League after finishing second in the league and Mokwena named Bucs players that he thought also deserved some mentioning.
“I’ve been surprised that some of our players have never been mentioned in the mix‚” said Mokwena to the publication.
“Without trying to sound like a cheerleader‚ but I think some of our players also deserve to be in and around the mix. Not to say that they deserve to win the awards," he added.
“Players like Musa Nyatama have been an exception and Innocent Maela has been an exception. We’ve seen him (Maela) contributing to about 65% as a left full back to the goals we have scored this season," he explained.
“But if you’re too much of a sportsman and without bringing any form of alliance‚ you probably should be giving it to Percy Tau," he concluded.
Pirates left-back Innocent Maela made the Defender of the Season shortlist, while his team-mate Nyatama was nominated for Midfielder of the Season award.
The PSL Awards ceremony will be held next week Tuesday.